Package: a4Base Exports: probe2gene, a4palette, filterVarInt, tTest, limmaTwoLevels, propDEgenes, histPvalue, histpvalueplotter, propdegenescalculation, volcanoPlot, volcanoplotter, lassoReg, logReg, probabilitiesPlot, plot1gene, plotCombination2genes, boxPlot, plotComb2Samples, plotCombMultSamples, profilesPlot, addQuantilesColors, combineTwoExpressionSet, computeLogRatio, plotLogRatio, createExpressionSet, replicates, heatmap.expressionSet ExportMethods: propDEgenes, histPvalue, volcanoPlot, topTable, spectralMap ExportClasses: ExpressionSetWithComputation Package: a4Classif Exports: lassoClass, pamClass, rfClass, ROCcurve Package: a4Core Exports: confusionMatrix, simulateData ExportMethods: topTable Package: a4Preproc Exports: addGeneInfo Package: a4Reporting Exports: annotationTable, generateEntrezIdLinks, generateGOIdLinks, print.xtableAnnotationTable ExportMethods: xtable ExportClasses: annotationTable Package: ABarray Exports: ABarray, ABarrayGUI, calcsn, concord, cvv, cvvPlot, doANOVA, doLPE, doPlotEset, doPlotFCT, doVennDiagram, drawVennDiagram, getMemberEset, getPantherMap, hclusterPlot, icpPlot, imputeFlag, lpe.fdr.BH, mamaplot, matrixPlot, mvaPair2, panel.cor, panel.scatter, qnNormalize, rgcolorsfunc, savejpg, scaleColorBar, snSummary Package: ABSSeq Exports: ABSSeq, GPTest, calPara, estimateSizeFactorsForMatrix, normalFactors, ABSDataSet, plotDifftoBase ExportMethods: results, sizeFactors, normMethod, groups, counts, sizeFactors<-, normMethod<-, groups<-, counts<- ExportClasses: ABSDataSet Package: ACME Exports: do.aGFF.calc, findRegions, read.resultsGFF, findClosestGene, write.bedGraph, write.sgr, getRefflat ExportMethods: show, print, plot, vals, threshold, cutpoints, chromosome, start, end ExportClasses: aGFF, aGFFCalc, ACMESet, ACMECalcSet Package: ADaCGH2 Exports: pSegmentDNAcopy, pSegmentWavelets, pSegmentHMM, pSegmentBioHMM, pSegmentGLAD, pSegmentCGHseg, pSegmentHaarSeg, pChromPlot, inputToADaCGH, outputToCGHregions, cutFile Package: adSplit Exports: adSplit, diana2means, drawRandomPS, randomDiana2means, makeEID2PROBESenv Package: affy Exports: .setAffyOptions ExportMethods: show, boxplot, image, exprs, featureNames, geneNames, sampleNames, se.exprs, updateObject ExportClasses: AffyBatch Package: affycomp Exports: affycomp, affycomp.compfig2, affycomp.compfig2b, affycomp.compfig3, affycomp.compfig4a, affycomp.compfig4b, affycomp.compfig4c, affycomp.compfig5a, affycomp.compfig5b, affycomp.compfig5c, affycomp.compfig5cde, affycomp.compfig5d, affycomp.compfig5e, affycomp.compfig7, affycomp.compfigs, affycomp.compfigs.calls, affycomp.figure1, affycomp.figure1b, affycomp.figure2, affycomp.figure2b, affycomp.figure3, affycomp.figure4a, affycomp.figure4b, affycomp.figure4c, affycomp.figure5a, affycomp.figure5b, affycomp.figure5c, affycomp.figure5d, affycomp.figure5e, affycomp.figure6a, affycomp.figure6b, affycomp.figure7, affycomp.figure.calls, affycomp.figures, affycompPlot, affycompTable, assessAll, assessDilution, assessFC, assessFC2, assessLS, assessMA, assessMA2, assessSD, assessSignal, assessSpikeIn, assessSpikeIn2, assessSpikeInSD, exprset.log, read.dilution, read.newspikein, read.spikein, remove.hgu133a.xhyb, tableAll, tableDilution, tableFC, tableFC2, tableLS, tableMA2, tableOverallSNR, tableRanks, tableSD, tableSignal, tableSpikeInSD Package: AffyCompatible ExportMethods: show Package: affyContam Exports: setCircRegion, setRectRegion, getCircRegion, getRectRegion Package: affycoretools Exports: affyLinks, affystart, annBM, entrezLinks, foldFilt, foldFiltBM, getMainProbes, getUniqueLL, goLinks, hyperG2annaffy, hyperGoutput, limma2annaffy, limma2biomaRt, makeGoTable, makeHmap, makeImages, makeVenn, maplot, mirna2mrna, outputRomer, plotDeg, plotHist, plotPCA, probes2table, probes2tableBM, runRomer, vennCounts2, vennPage, vennSelect, vennSelect2, vennSelectBM, vennSelectFC, writeFit Package: AffyExpress Exports: AffyInteraction, AffyQA, AffyRegress, Filter, interaction.result2html, make.contrast, make.design, post.interaction, pre.process, regress, result2html, select.sig.gene, import.data Package: affyPara Exports: distributeFiles, removeDistributedFiles, read.affybatchPara, splitAffyBatch, splitFileVector, splitMatrix, bgCorrectPara, normalizeAffyBatchQuantilesPara, normalizeAffyBatchInvariantsetPara, normalizeAffyBatchConstantPara, normalizeAffyBatchLoessPara, normalizeAffyBatchLoessIterPara, vsn2Para, justvsnPara, vsnrmaPara, computeExprSetPara, preproPara, rmaPara, mergeAffyBatches, combineMatrices, boxplotPara, MAplotPara, MAplotSer, summaryM1M2Para, makeCluster, stopCluster Package: affyPLM ExportClasses: PLMset Package: affyQCReport Exports: affyQAReport, borderQC1, borderQC2, correlationPlot, openQAReport, QCReport, rmQAReport, signalDist, titlePage Package: AffyRNADegradation Exports: RNADegradation, PlotTongs, GetTongs, PlotDegradationHooks ExportMethods: plotDx, d, afbatch ExportClasses: AffyDegradationBatch Package: AffyTiling Exports: AnalyzeTilingCelFiles, TilingCelFiles2Probesets, AssociateWithGenes, AssociateWithInterval, parseBPMAP Package: AGDEX Exports: make.dex.set.object, agdex, write.agdex.result, read.agdex.result, agdex.scatterplot, get.gset.result.details, read.agdex.gset.details, write.agdex.gset.details Package: agilp Exports: AAProcess, AALoess, Baseline, Equaliser, filenamex, Loader, IDswop Package: AgiMicroRna Exports: readMicroRnaAFE, readTargets, qcPlots, boxplotMicroRna, plotDensityMicroRna, RleMicroRna, mvaMicroRna, mvaBASIC, hierclusMicroRna, HeatMapMicroRna, PCAplotMicroRna, cvArray, tgsMicroRna, tgsNormalization, rmaMicroRna, filterMicroRna, esetMicroRna, writeEset, basicLimma, getDecideTests, pvalHistogram, significantMicroRna ExportMethods: show ExportClasses: uRNAList Package: ALDEx2 Exports: aldex ExportMethods: getMonteCarloInstances, getSampleIDs, getFeatures, numFeatures, numMCInstances, getFeatureNames, getReads, numConditions, getMonteCarloReplicate Package: AllelicImbalance Exports: alleleCounts<-, genotype<-, ASEsetFromCountList, RBias, alleleCounts, arank, barplotLatticeCounts, barplotLatticeFraction, countsPerSample, countsPerSnp, coverageMatrixListFromGAL, decorateWithExons, decorateWithGenes, defaultMapBias, detectAI, fraction, frequency, genotype, getAlleleCounts, getAnnotationDataFrame, getAreaFromGeneNames, getCDSFromAnnotation, getCDSVector, getDefaultMapBiasExpMean, getExonsFromAnnotation, getExonsVector, getGenesFromAnnotation, getGenesVector, getSnpIdFromLocation, getTranscriptsFromAnnotation, getTranscriptsVector, hetPerSample, hetPerSnp, impBamGAL, impBamGRL, impBcfGR, impBcfGRL, implodeList, mapBias, realCigarPosition, realCigarPositions, realCigarPositionsList, refbiasByAnnotation, scanForHeterozygotes ExportMethods: show, refbiasByAnnotation, refFraction, refAllele, mapBias, locationplot, lbarplot, inferGenotypes, inferAlleles, hetPerSnp, hetPerSample, hetFilt, glocationplot, genotype, frequency, fraction, detectAI, defaultMapBias, countsPerSnp, countsPerSample, chisq.test, binom.test, barplot, arank, alleleCounts, CoverageDataTrack, ASEDAnnotationTrack, genotype<-, alleleCounts<- ExportClasses: ReferenceBias, ASEset Package: alsace Exports: splitTimeWindow, mergeTimeWindows, smallComps, removeComps, combineComps, suggestCompCombis, correctPeaks, correctRT, doALS, getTime, getWavelength, findpeaks, fitpeaks, filterPeaks, getAllPeaks, getPeakTable, opa, preprocess, showALSresult Package: annaffy Exports: selectorWidget, is.annpkg ExportMethods: colnames, colnames<-, getCSS, getHTML, getTD, getText, getURL, probeids, probeids<-, saveHTML, saveText, show, [, [[ ExportClasses: aafChromLoc, aafChromosome, aafCytoband, aafDescription, aafGenBank, aafGO, aafGOItem, aafIntensity, aafList, aafLocusLink, aafPathway, aafPathwayItem, aafProbe, aafPubMed, aafSigned, aafSymbol, aafTable, aafUniGene Package: annotate Exports: .buildAnnotateOpts, .getIdTag, .getNcbiURL, .handleXML, .efetch, .transformAccession, ACC2homology, accessionToUID, ACCNUMStats, annPkgName, aqListGOIDs, buildChromLocation, buildPubMedAbst, checkArgs, chrCats, compatibleVersions, createLLChrCats, createMAPIncMat, dropECode, filterGOByOntology, findChr4LL, findNeighbors, genbank, getAnnMap, getBoundary, getEG, getEvidence, getGI, getGO, getGOChildren, getGOdesc, getGOOntology, getGOParents, getGOTerm, getGPLNames, getLL, getOntology, getOrgNameNCode, getPMID, getPMInfo, getQueryLink, getSAGEFileInfo, getSAGEGPL, getSEQ, getSYMBOL, getUniqAnnItem, getValidChr, GO2heatmap, GOmnplot, hasGOannote, HGID2homology, homoData, htmlpage, KEGG2heatmap, KEGGmnplot, LL2homology, lookUp, makeAnchor, mapOrgs, p2LL, pm.abstGrep, pm.getabst, pm.titles, pmAbst2HTML, pmid2MIAME, PMIDAmat, pmidQuery, probesByLL, pubmed, PWAmat, readGEOAnn, readIDNAcc, readUrl, serializeDataPkgEnvs, serializeEnv, UniGeneQuery, entrezGeneByID, entrezGeneQuery, usedChromGenes, usedChromGenes, weightByConfi, whatACC, setRepository, getRepositories, clearRepository, isValidKey, allValidKeys, updateSymbolsToValidKeys, blastSequences ExportMethods: abstText, articleTitle, authors, chromInfo, chromLengths, chromLocs, chromNames, dataSource, Definition, fileName, geneSymbols, GOID, homoACC, homoHGID, homoLL, homoOrg, homoPS, homoType, homoURL, initialize, journal, mainPage, nChrom, Ontology, organism, pageText, pageTitle, pmid, probesToChrom, pubDate, pubMedAbst, Secondary, show, sidePage, Synonym, Term, toFile, topPage ExportClasses: chromLocation, FramedHTMLPage, homoData, HTMLPage, pubMedAbst Package: AnnotationDbi Exports: unlist2, showQCData, debugSQL, GOTerms, makeGOGraph, dbFileConnect, dbFileDisconnect, mergeToNamespaceAndExport, createAnnObjs.SchemaChoice, checkMAPCOUNTS, make_eg_to_go_map, make_go_to_eg_map, toSQLStringSet, inpIDMapper, intraIDMapper, idConverter, metadata, supportedSeqnameMappings, findSequenceRenamingMaps, supportedSeqnameStyles, extractSeqnameSet, testSeqnames, isSupportedSeqnamesStyle, listAllSupportedStylesBySpecies, listAllSupportedSeqnameStyles, supportedSeqnames, species, createSimpleBimap ExportMethods: dbconn, dbfile, dbmeta, dbschema, dbInfo, direction, direction<-, revmap, colnames, colmetanames, Lkeyname, Rkeyname, keyname, tagname, Rattribnames, Rattribnames<-, Lkeys, Rkeys, keys, Lkeys<-, Rkeys<-, keys<-, subset, [, Llength, Rlength, length, isNA, mappedLkeys, mappedRkeys, mappedkeys, count.mappedLkeys, count.mappedRkeys, count.mappedkeys, show, summary, toTable, as.data.frame, head, tail, nrow, links, count.links, nhit, ncol, dim, toggleProbes, hasMultiProbes, hasSingleProbes, getBimapFilters, setInpBimapFilter, GOID, Term, Ontology, Synonym, Secondary, Definition, GOFrame, GOAllFrame, getGOFrameData, KEGGFrame, getKEGGFrameData, as.list, as.character, ls, mget, eapply, get, exists, [[, $, contents, sample, initialize, saveDb, loadDb, species, columns, keytypes, select ExportClasses: Bimap, FlatBimap, AnnObj, AnnDbObj, L2Rlink, AnnDbBimap, GoAnnDbBimap, Go3AnnDbBimap, GOTermsAnnDbBimap, AnnDbMap, IpiAnnDbMap, AgiAnnDbMap, ProbeAnnDbBimap, ProbeAnnDbMap, ProbeIpiAnnDbMap, ProbeGo3AnnDbBimap, AnnotationDb, OrgDb, ChipDb, InparanoidDb, GODb, ReactomeDb, GOTerms, GOFrame, GOAllFrame, KEGGFrame Package: AnnotationForge Exports: loadAnnDbPkgIndex, populateDB, makeDBPackage, available.db0pkgs, available.dbschemas, available.chipdbschemas, wrapBaseDBPackages, makeOrgPackageFromNCBI, makeOrgPackage, makeChipPackage, getProbeDataAffy, getProbeData_1lq, makeProbePackage, makeInpDb ExportMethods: makeAnnDbPkg ExportClasses: AnnDbPkgSeed Package: AnnotationFuncs Exports: translate, pickRefSeq, pickRefSeq.Protein, pickRefSeq.mRNA, mapLists, removeNAs, pickGO, getEvidenceCodes, getOrthologs Package: AnnotationHub Exports: AnnotationHub, ahinfo ExportMethods: $, [[, [, as.list, filters, filters<-, hubUrl, hubCache, hubCache<-, hubResource, keys, keytypes, columns, length, metadata, subset, query, names, possibleDates, show, snapshotDate, snapshotDate<-, snapshotPaths, snapshotUrl, snapshotUrls, snapshotVersion, display Package: annotationTools Exports: compactList, getANNOTATION, getGENEID, getGENEONTOLOGY, getGENESYMBOL, getGENETITLE, getHOMOLOG, getMULTIANNOTATION, getOrthologousProbesets, getPROBESET, listToCharacterVector, ps2ps Package: anota Exports: anotaPerformQc, anotaResidOutlierTest, anotaGetSigGenes, anotaPlotSigGenes Package: antiProfiles Exports: apStats ExportMethods: getProbesetIds, getProbeStats, getNormalTissueRegions, getNormalRegions, buildAntiProfile, apReorder, apCount ExportClasses: TissueSpecAntiProfile, AntiProfileStats, AntiProfile Package: apComplex Exports: bhmaxSubgraph, findComplexes, mergeComplexes, plotComplex, sortComplexes Package: ArrayExpress Exports: ArrayExpress, getAE, queryAE, ae2bioc, getcolproc, getcolraw, procset, extract.zip Package: ArrayExpressHTS Exports: ArrayExpressHTS, ArrayExpressHTSFastQ, prepareReference, prepareAnnotation, getPipelineOptions, getPipelineOption, setPipelineOptions, isRCloud, getDefaultProcessingOptions, getDefaultRCloudOptions, getDefaultFilteringOptions Package: arrayMvout ExportMethods: ArrayOutliers, plot, show ExportClasses: arrOutStruct Package: arrayQuality Exports: readAgilent, readcontrolCode, agQuality, EMSplit, getSpikeIds, getSpikeIndex, gpQuality, globalQuality, maQualityPlots, meeboQuality, meeboQualityPlots, heeboQuality, heeboQualityPlots, PRv9mers, PRvQCHyb, qualBoxplot, qualityScore, qcScore, readGPR, readSpikeTypes, readSpot, slideQuality, scaleRefTable, spotQuality, HeeboSpotTypes, MeeboSpotTypes, controlCodeHeebo, controlCodeMeebo Package: arrayQualityMetrics Exports: arrayQualityMetrics, prepdata, prepaffy, aqm.writereport, aqm.boxplot, aqm.maplot, aqm.density, aqm.probesmap, aqm.meansd, aqm.heatmap, aqm.pca, aqm.rle, aqm.nuse, aqm.rnadeg, aqm.pmmm, aqm.spatial, addXYfromGAL, outliers, boxplotOutliers ExportClasses: aqmReportModule, outlierDetection Package: ArrayTools Exports: createExpressionSet, createIndex, geneFilter, regress, postInteraction, createIngenuityFile, output.gct, output.cls, output.ing, createGSEAFiles, adjustment, getAdjP, getDesign, getAnnotation, getCompare1, getCompare2, getContrast, getCovariates, getF, getFC, getFCCutoff, getFilterMethod, getID, getIndex, getInteraction, getIntIndex, getLength, getLevel, getTarget, getNormalizationMethod, getP, getPCutoff, Output2HTML, qa3prime, qaGeneST, regressionMethod, selectSigGene, Sort, preProcessGeneST, preProcess3prime, selectSigGene, selectSigGeneInt ExportMethods: adjustment, getAdjP, getAnnotation, getContrast, getF, getFC, getFCCutoff, getFilterMethod, getID, getIndex, getNormalizationMethod, getP, getPCutoff, Output2HTML, regressionMethod, show, Sort, summary, getLength, getCompare1, getCompare2, getInteraction, getLevel, initialize, getCovariates, getDesign, getIntIndex, getTarget ExportClasses: regressResult, interactionResult, designMatrix, contrastMatrix Package: ArrayTV Exports: gcCorrectMain ExportMethods: gcCorrect Package: ARRmNormalization Exports: getDesignInfo, getBackground, getQuantiles, getCoefficients, positionPlots, quantilePlots, normalizeARRm Package: ASEB Exports: SequenceInfo, readSequence, asebSites, asebProteins, drawStat, drawEScurve Package: ASGSCA Exports: GSCA, GSCAestim Package: asmn Exports: norm_factors, normalize_asmn Package: ASSET Exports: h.traits, h.types, h.summary, h.forestPlot, z.max, p.dlm, p.tube Package: ASSIGN Exports: assign.preprocess, assign.mcmc, assign.convergence, assign.summary, assign.cv.output, assign.output, assign.wrapper Package: AtlasRDF Exports: getAllEnsemblGenesForExFactor, getSpeciesSpecificEnsemblGenesForExFactor, getExperimentsByDescription, getGenesForExperimentID, getGenesForExperimentURI, getExperimentURIsForGeneId, getExperimentIdsForGeneURI, getLabel, getPathwaysFromGenesAndCondition, drawHeatMapForAtlasExperiment, getOntologyMappings, getGeneListFromPubmedid, getGenesForPathwayURI, getPathwayForGeneId, getRankedPathwaysForGeneIds, searchForEFOTerms, getGeneUriFromName, getExFactorURIFromLabel, searchForEFOTerms, getGeneUriFromEnsemblId, getPathwayUriFromName, doFishersEnrichment, doFishersEnrichmentForGeneNames, doFishersEnrichmentForEnsemblIds, vizPvalues, excludeSubclasses, includeOnlySubclasses, getTaxonURI, orderEnrichmentResults ExportClasses: generef, pathwayresult, factorbackground, enrichmentresult Package: attract ExportClasses: SynExpressionSet, AttractorModuleSet Package: BADER Exports: BADER Package: BAGS Exports: DataGeneSets, Gibbs5, Gibbs4, Gibbs3, Gibbs2, MCMCDataSet, ReadGMT Package: ballgown Exports: expr<-, indexes<-, pData<-, annotate_assembly, ballgown, ballgownrsem, checkAssembledTx, clusterTranscripts, collapseTranscripts, contains, dirs, eexpr, expr, exprfilter, geneIDs, geneNames, getAttributeField, getGenes, gexpr, gffRead, gffReadGR, iexpr, indexes, last, mergedDate, pData, pctOverlap, plotLatentTranscripts, plotMeans, plotTranscripts, sampleNames, seqnames, stattest, structure, subset, texpr, transcriptIDs, transcriptNames, writeFiles ExportMethods: transcriptNames, transcriptIDs, texpr, subset, structure, seqnames, sampleNames, pData, mergedDate, indexes, iexpr, gexpr, geneNames, geneIDs, expr, eexpr, dirs, pData<-, indexes<-, expr<- ExportClasses: ballgown Package: BaseSpaceR Exports: ServiceURI, ResponseStatus, AppAuth, performOAuth, authWebClient, authNativeClient, uri, initializeAuth, requestAccessToken, hasAccess, Id, Name, Href, DateCreated, UserOwnedBy, Status, HrefBaseSpaceUI, Items, DisplayedCount, TotalCount, Offset, Limit, SortDir, SortBy, auth, Users, userItem, Runs, listRuns, runItem, runCollection, Projects, listProjects, projectItem, projectCollection, createProject, Samples, listSamples, sampleItem, sampleCollection, AppResults, appResultItem, appResultCollection, listAppResults, createAppResults, AppSessions, listAppSessions, updateAppSessions, Genomes, listGenomes, genomeItem, genomeCollection, Files, listFiles, fileItem, fileCollection, getFiles, putFiles, getIndexedBam, getBAMs, countRuns, countProjects, countSamples, countAppResults, countAppSessions, countGenomes, countFiles, getVariantSet, getVariants, getCoverage, getCoverageStats ExportMethods: uri, initializeAuth, requestAccessToken, hasAccess, Id, Name, Href, DateCreated, UserOwnedBy, Status, HrefBaseSpaceUI, Items, DisplayedCount, TotalCount, Offset, Limit, SortDir, SortBy, auth, Users, Runs, listRuns, Projects, listProjects, createProject, Samples, listSamples, AppResults, listAppResults, createAppResults, AppSessions, listAppSessions, updateAppSessions, Genomes, listGenomes, Files, listFiles, getFiles, putFiles, getBAMs, countRuns, countProjects, countSamples, countAppResults, countAppSessions, countGenomes, countFiles, getVariantSet, getVariants, getCoverage, getCoverageStats, $, show, as.list ExportClasses: ServiceURI, ResponseStatus, AppAuth, AppSessionAuth, Item, Collection, Response, Users, userItem, Runs, RunsSummary, runItem, runCollection, Genomes, GenomesSummary, genomeItem, genomeCollection, Projects, ProjectsSummary, projectItem, projectCollection, Samples, SamplesSummary, sampleItem, sampleCollection, AppResults, AppResultsSummary, appResultItem, appResultCollection, AppSessions, appSessionItem, Files, FilesSummary, fileItem, fileCollection Package: Basic4Cseq ExportMethods: prepare4CseqData, createVirtualFragmentLibrary, printBEDFragmentLibrary, checkRestrictionEnzymeSequence, giveEnzymeSequence, readPointsOfInterestFile, readsToFragments, chooseNearCisFragments, normalizeFragmentData, getReadDistribution, visualizeViewpoint, drawHeatmap, exportVisualizationFragmentData, importVisualizationFragmentData, printWigFile, simulateDigestion, drawDigestionFragmentHistogram, plotTransInteractions, Data4Cseq, viewpointChromosome, viewpointChromosome<-, viewpointInterval, viewpointInterval<-, readLength, readLength<-, pointsOfInterest, pointsOfInterest<-, rawReads, rawReads<-, rawFragments, rawFragments<-, nearCisFragments, nearCisFragments<- ExportClasses: Data4Cseq Package: BayesPeak Exports: bayespeak, summarise.peaks, summarize.peaks, read.bed, plot.overfitdiag, identify.overfitdiag, region.overfitdiag, plot.bed, plot.job, plot.PP Package: baySeq ExportClasses: countData Package: BCRANK Exports: bcrank, matchingSites ExportMethods: show, toptable, fname, searchPath, pwm, plot, bcrankScore, consensus, matchVector ExportClasses: BCRANKmatch, BCRANKsearch, BCRANKresult Package: beadarray Exports: insertBeadData, removeBeadData, getBeadData, plotChipLayout, createTargetsFile, quickSummary, summarize, identifyControlBeads, insertSectionData, backgroundCorrectSingleSection, beadarrayUsersGuide, suggestAnnotation, addFeatureData, readIllumina, readLocsFile, convertBeadLevelList, readIdatFiles, processSwathData, readTIFF, plotTIFF, illuminaForeground, illuminaBackground, illuminaSharpen, medianBackground, logGreenChannelTransform, logRedChannelTransform, logRatioTransform, greenChannelTransform, redChannelTransform, greenChannel, plotBeadIntensities, genericBeadIntensityPlot, poscontPlot, outlierplot, imageplot, checkRegistration, makeQCTable, expressionQCPipeline, calculateOutlierStats, controlProbeDetection, plotBeadLocations, makeControlProfile, combinedControlPlot, BASH, HULK, generateNeighbours, BASHCompact, BASHDiffuse, BASHExtended, setWeights, showArrayMask, readBeadSummaryData, normaliseIllumina, medianNormalise, calculateDetection, checkPlatform, getAnnotation, setAnnotation, beadStatusVector, plotMAXY, illuminaOutlierMethod, squeezedVarOutlierMethod, weightsOutlierMethod, noOutlierMethod, readSampleSheet, makeGEOSubmissionFiles, createGEOMeta, createGEOMatrix, limmaDE ExportMethods: metrics, p95, snr, show, [[, dim, sectionNames, numBeads, boxplot, exprs, se.exprs, nObservations, Detection, annotation, annotation<-, se.exprs<-, exprs<-, nObservations<-, Detection<-, qcData, combine, DesignMatrix, ContrastMatrix, ArrayWeights, LogFC, LogOdds, PValue, ArrayWeights<-, LogFC<-, LogOdds<-, PValue<-, DesignMatrix<-, ContrastMatrix<- ExportClasses: BeadLevelList, beadLevelData, ExpressionSetIllumina, illuminaChannel, beadRegistrationData, limmaResults Package: beadarraySNP Exports: read.SnpSetIllumina, backgroundEstimate, backgroundCorrect.SNP, normalizeBetweenAlleles.SNP, normalizeBetweenSubsamples.SNP, normalizeWithinArrays.SNP, normalizeLoci.SNP, RG2polar, polar2RG, standardNormalization, heterozygousSNPs, compareGenotypes, heterozygosity, reportSamplesSmoothCopyNumber, reportChromosomesSmoothCopyNumber, pdfSamplesSmoothCopyNumber, pdfChromosomesSmoothCopyNumber, removeLowQualityProbes, removeLowQualitySamples, calculateQCarray, pdfQC, smoothed.intensity, renameOPA, calculateLOH, reportGenomeGainLossLOH, pdfChromosomeGainLossLOH, reportChromosomeGainLossLOH, reportGenomeIntensityPlot, convert2aCGH, convert2SegList, segmentate, reportGenotypeSegmentation, plotGoldenGate4OPA, plotGenomePanels, createCNSummary, alterCN, getDNAindex, interactiveCNselect, setRealCN, Sample_Map2Samplesheet, pdfBeadstudioQC, BeadstudioQC, calculateLair, GetBeadStudioSampleNames, dist.GT, calculateSmooth ExportMethods: [, [[, $, annotation, combine, experimentData, exprs, featureNames, pData, phenoData, sampleNames, samples, featureData, sortGenomic, annotation<-, description<-, experimentData<-, exprs<-, featureNames<-, pData<-, phenoData<-, sampleNames<-, assayData<-, featureData<-, fData, fData<-, dim, assayData, initialize, arrayType<-, arrayID<-, arrayType, arrayID, plotQC, reportSamplePanelQC, calculateGSR, cn.segments, cn.segments<- ExportClasses: SnpSetIllumina, SnpSetSegments, QCIllumina Package: BeadDataPackR Exports: decompressBeadData, compressBeadData, readCompressedData, extractLocsFile Package: BEAT Exports: makeParams, positions_to_regions, generate_results, epimutation_calls Package: betr Exports: betr Package: bgafun Exports: convert_aln_amino, convert_aln_AAP, average_cols_aap, remove_gaps_groups, add_pseudo_counts, run_between_pca, top_residues_2_groups, create_profile_strings, Calculate_Row_Weights Package: BGmix Exports: BGmix, ccSummary, ccTrace, ccParams, ccPred, plotCompare, plotBasic, plotTrace, plotFDR, plotPredChecks, plotMixDensity, calcFDR, TailPP, histTailPP, FDRforTailPP, FDRplotTailPP, EstimatePi0, readBGX Package: bgx Exports: bgx, standalone.bgx, readOutput.bgx, plotExpressionDensity, plotDEDensity, plotDEHistogram, rankByDE, plotDiffRank Package: BHC Exports: bhc, WriteOutClusterLabels, DiscretiseData, FindOptimalBinning Package: BicARE Exports: FLOC, bicluster, testAnnot, testSet, residue, makeReport Package: bigmemoryExtras Exports: BigMatrix, BigMatrixFactor, attachAssayDataElements, updateAssayDataElementPaths, updateBackingfiles, updateBigMatrix ExportMethods: nrow, nlevels, ncol, levels, length, dimnames, dim, as.matrix, apply, annotatedDataFrameFrom, levels<-, dimnames<-, [<-, [ ExportClasses: BigMatrixFactor, BigMatrix Package: bioassayR Exports: connectBioassayDB, addDataSource, loadBioassay, dropBioassay, disconnectBioassayDB, newBioassayDB, addBioassayIndex, dropBioassayIndex, activeTargets, activeAgainst, selectiveAgainst, getAssay, getAssays, parsePubChemBioassay, activityMatrix, getBioassaySetByCids, perTargetMatrix ExportMethods: queryBioassayDB, show, aid, source_id, assay_type, organism, scoring, targets, target_types, scores, aid<-, source_id<-, assay_type<-, organism<-, scoring<-, targets<-, target_types<-, scores<- ExportClasses: BioassayDB, bioassay, bioassaySet Package: Biobase Exports: Aggregate, addVigs2WinMenu, anyMissing, as.data.frame.ExpressionSet, assayDataNew, assayDataValidMembers, assayDataElementNames, assayDataElement, assayDataElementReplace, assayDataElement<-, cache, copyEnv, copySubstitute, createPackage, dumpPackTxt, esApply, getPkgVigs, isUnique, listLen, matchpt, mkScalar, multiassign, NChannelSet, note, openPDF, openVignette, package.version, reverseSplit, rowMax, rowMedians, rowMin, rowQ, readExpressionSet, read.AnnotatedDataFrame, read.MIAME, MIAME, selectSome, strbreak, subListExtract, testBioCConnection, lcSuffix, lcPrefix, lcPrefixC, updateOldESet, userQuery, validMsg ExportMethods: [, [[, $, abstract, aggenv, aggfun, annotatedDataFrameFrom, annotation, channel, channelNames, coerce, combine, content, contents, description, dimnames, dimnames<-, dims, experimentData, expinfo, exprs, featureNames, featureData, fData, fvarLabels, fvarMetadata, hybridizations, initfun, length, locked, makeDataPackage, normControls, notes, otherInfo, pData, phenoData, preproc, protocolData, sampleNames, samples, se.exprs, selectChannels, snpCall, snpCallProbability, storageMode, varLabels, varMetadata, annotation<-, channelNames<-, description<-, dimLabels<-, experimentData<-, exprs<-, featureNames<-, featureData<-, fData<-, fvarLabels<-, fvarMetadata<-, notes<-, preproc<-, pData<-, phenoData<-, protocolData<-, sampleNames<-, snpCall<-, snpCallProbability<-, varLabels<-, varMetadata<-, assayData<-, se.exprs<-, storageMode<-, write.exprs, dim, dimLabels, assayData, pubMedIds, pubMedIds<-, isVersioned, isCurrent, classVersion, classVersion<-, updateObject, updateObjectTo, initialize, show, Compare, AnnotatedDataFrame, ExpressionSet ExportClasses: aggregator, container, eSet, MIAxE, MIAME, characterORMIAME, annotatedDataset, AssayData, data.frameOrNULL, AnnotatedDataFrame, Versions, VersionsNull, Versioned, VersionedBiobase, ExpressionSet, MultiSet, SnpSet, NChannelSet, ScalarObject, ScalarInteger, ScalarLogical, ScalarNumeric, ScalarCharacter Package: BiocCaseStudies Exports: parseLibVers, requiredPackages, packages2install, resample, mySessionInfo, fixedWidthCat, lcol1, lcol2, lcol3, dcol1, dcol2, dcol3, numName, sepInt Package: BiocCheck Exports: BiocCheck, usage Package: BiocGenerics Exports: append, as.data.frame, as.list, as.vector, cbind, rbind, do.call, duplicated, anyDuplicated, eval, evalq, pmax, pmin, pmax.int, pmin.int, Reduce, Filter, Find, Map, Position, get, mget, is.unsorted, lapply, sapply, mapply, match, nrow, ncol, NROW, NCOL, order, paste, rank, rep.int, rownames, rownames<-, colnames, colnames<-, union, intersect, setdiff, sort, start, start<-, end, end<-, width, width<-, table, tapply, unique, unlist, unsplit, relist, boxplot, image, density, residuals, weights, xtabs, clusterCall, clusterApply, clusterApplyLB, clusterEvalQ, clusterExport, clusterMap, clusterSplit, parLapply, parSapply, parApply, parRapply, parCapply, parLapplyLB, parSapplyLB, annotation, annotation<-, combine, normalize, strand, strand<-, updateObject, updateObjectFromSlots, getObjectSlots, unstrand ExportMethods: combine, updateObject, counts, counts<-, design, design<-, dispTable, dispTable<-, sizeFactors, sizeFactors<-, conditions, conditions<-, estimateSizeFactors, estimateDispersions, plotDispEsts, plotMA ExportClasses: connection, file, url, gzfile, bzfile, unz, pipe, fifo, sockconn, terminal, textConnection, gzcon, characterORconnection, AsIs Package: biocGraph Exports: imageMap Package: BiocInstaller Exports: biocLite, biocVersion, biocUpdatePackages, biocinstallRepos, useDevel, biocValid, monograph_group, RBioinf_group, biocases_group, all_group Package: BiocParallel Exports: MulticoreParam, SnowParam, DoparParam, SerialParam, BatchJobsParam, bplapply, bpvec, bpvectorize, bpmapply, bpaggregate, bpiterate, bpworkers, bpbackend, bpbackend<-, bpstart, bpstop, bpisup, bpschedule, register, registered, bpparam, bpresume, bplasterror, multicoreWorkers, snowWorkers ExportMethods: show ExportClasses: BiocParallelParam, MulticoreParam, SnowParam, DoparParam, SerialParam, BatchJobsParam Package: BiocStyle Exports: latex, markdown, Biocpkg, Biocannopkg, Biocexptpkg, CRANpkg, Rpackage, Githubpkg, html_document, pdf_document Package: biocViews Exports: writeBiocViews, getBiocViews, write_VIEWS, write_REPOSITORY, genReposControlFiles, extractVignettes, extractManuals, extractCitations, getCurrentbiocViews, extractNEWS, extractHTMLDocuments, extractTopLevelFiles, writeRepositoryHtml, writePackageDetailHtml, getSubTerms, getBiocSubViews, validate_bioc_views, writeTopLevelView, writeHtmlDoc, write_SYMBOLS, writeRFilesFromVignettes, getPackageNEWS, printNEWS, recommendBiocViews ExportMethods: coerce, show, htmlDoc, htmlValue, htmlFilename ExportClasses: Htmlized, PackageDetail, pdAuthorMaintainerInfo, pdVignetteInfo, pdDownloadInfo, pdDetailsInfo, pdDescriptionInfo, pdVigsAndDownloads, RepositoryDetail, rdPackageTable, BiocView, bvTitle, bvPackageTable, bvSubViews, bvParentViews Package: bioDist Exports: cor.dist, spearman.dist, tau.dist, euc, man, mutualInfo, KLdist.matrix, KLD.matrix, closest.top, MIdist ExportMethods: KLD.matrix, KLdist.matrix, cor.dist, euc, man, mutualInfo, MIdist, spearman.dist, tau.dist Package: biomaRt Exports: listMarts, getGene, getSequence, exportFASTA, useMart, listDatasets, useDataset, listAttributes, listFilters, getBM, getXML, getLDS, attributePages, filterOptions, filterType, getBMlist, NP2009code, keys, columns, keytypes, select ExportMethods: show ExportClasses: Mart Package: BioMVCClass ExportMethods: ordering, grLayout, rNames, ordering<-, grLayout<-, rNames<-, incidMat, gTestStat, gsTestStat, expData, descr, incidMat<-, gTestStat<-, gsTestStat<-, expData<-, descr<- ExportClasses: graphModel, exprModel, graphView, heatmapView, GSE, gseModel Package: biomvRCNS Exports: biomvRhsmm, hsmmRun, sojournAnno, biomvRseg, regionSegCost, regionSegAlphaNB, biomvRmgmr, maxGapminRun, biomvRGviz, splitFarNeighbour, simSegData ExportMethods: plot, show ExportClasses: biomvRCNS Package: BioNet Exports: saveNetwork, loadNetwork.sif, loadNetwork.tab, rmSelfLoops, makeNetwork, subNetwork, largestComp, largestScoreComp, permutateNodes, compareNetworks, getEdgeList, writeHeinzEdges, writeHeinzNodes, writeHeinz, runHeinz, scanFDR, readHeinzTree, readHeinzGraph, runFastHeinz, mapByVar, plot.bum, hist.bum, plotLLSurface, plotModule, plot3dModule, save3dModule, aggrPvals, fbum, fbumLL, bumOptim, print.bum, summary.bum, fitBumModel, fdrThreshold, piUpper, scoreOffset, scoreFunction, scoreNodes, getCompScores, resamplingPvalues, consensusScores, sortedEdgeList Package: BioSeqClass Exports: getTrain, hr, distance, elements, aaClass, featureBinary, featureCTD, featureFragmentComposition, featureGapPairComposition, featureCKSAAP, featureHydro, featureACH, featureAAindex, featureACI, featureACF, featurePseudoAAComp, featurePSSM, featureDOMAIN, featureSSC, getDSSP, predictPROTEUS, predictPFAM, featureBDNAVIDEO, featureDIPRODB, classifyModelLIBSVM, classifyModelSVMLIGHT, classifyModelNB, classifyModelRF, classifyModelKNN, classifyModelTree, classifyModelRPART, classifyModelCTREE, classifyModelCTREELIBSVM, classifyModelBAG, classifyModelNNET, performance, classify, selectFFS, selectWeka, featureEvaluate Package: Biostrings Exports: IUPAC_CODE_MAP, mergeIUPACLetters, AMINO_ACID_CODE, AA_ALPHABET, AA_STANDARD, AA_PROTEINOGENIC, GENETIC_CODE, RNA_GENETIC_CODE, GENETIC_CODE_TABLE, getGeneticCode, DNA_BASES, RNA_BASES, DNA_ALPHABET, RNA_ALPHABET, seqtype, seqtype<-, get_seqtype_conversion_lookup, alphabet, BString, DNAString, RNAString, AAString, BStringSet, DNAStringSet, RNAStringSet, AAStringSet, unmasked, BStringSetList, DNAStringSetList, RNAStringSetList, AAStringSetList, xscat, partitioning, readBStringSet, readDNAStringSet, readRNAStringSet, readAAStringSet, fasta.info, fastq.geometry, writeXStringSet, saveXStringSet, letter, getSeq, letterFrequency, letterFrequencyInSlidingView, alphabetFrequency, hasOnlyBaseLetters, uniqueLetters, consensusMatrix, consensusString, mkAllStrings, oligonucleotideFrequency, dinucleotideFrequency, trinucleotideFrequency, nucleotideFrequencyAt, oligonucleotideTransitions, twoWayAlphabetFrequency, dinucleotideFrequencyTest, complement, reverseComplement, translate, codons, toComplex, extractAt, replaceAt, replaceLetterAt, .inplaceReplaceLetterAt, injectHardMask, padAndClip, stackStrings, N50, transcribe, cDNA, dna2rna, rna2dna, width0, startIndex, endIndex, extractAllMatches, neditStartingAt, neditEndingAt, neditAt, isMatchingStartingAt, isMatchingEndingAt, isMatchingAt, which.isMatchingStartingAt, which.isMatchingEndingAt, which.isMatchingAt, hasLetterAt, mismatch, nmatch, nmismatch, gregexpr2, matchPattern, countPattern, vmatchPattern, vcountPattern, maskMotif, mask, matchLRPatterns, trimLRPatterns, matchProbePair, maxWeights, minWeights, maxScore, minScore, unitScale, PWM, PWMscoreStartingAt, matchPWM, countPWM, findPalindromes, findComplementedPalindromes, palindromeArmLength, complementedPalindromeArmLength, palindromeLeftArm, complementedPalindromeLeftArm, palindromeRightArm, complementedPalindromeRightArm, tb, tb.width, nnodes, hasAllFlinks, computeAllFlinks, patternFrequency, PDict, matchPDict, countPDict, whichPDict, vmatchPDict, vcountPDict, vwhichPDict, countIndex, subpatterns, pattern, PhredQuality, SolexaQuality, IlluminaQuality, encoding, quality, QualityScaledBStringSet, QualityScaledDNAStringSet, QualityScaledRNAStringSet, QualityScaledAAStringSet, insertion, deletion, unaligned, aligned, indel, nindel, PairwiseAlignments, type, pid, PairwiseAlignmentsSingleSubject, writePairwiseAlignments, nedit, mismatchTable, mismatchSummary, compareStrings, lcprefix, lcsuffix, pmatchPattern, lcsubstr, nucleotideSubstitutionMatrix, errorSubstitutionMatrices, qualitySubstitutionMatrices, pairwiseAlignment, stringDist, DNAMultipleAlignment, RNAMultipleAlignment, AAMultipleAlignment, rowmask, rowmask<-, colmask, colmask<-, maskGaps, maskednrow, maskedncol, maskeddim, readDNAMultipleAlignment, readRNAMultipleAlignment, readAAMultipleAlignment, consensusViews, write.phylip, detail, needwunsQS, longestConsecutive, matchprobes ExportMethods: length, [, rep, coerce, as.integer, as.numeric, as.character, as.matrix, toString, show, summary, start, end, width, Views, subpatterns, pattern, quality, encoding, insertion, deletion, unaligned, aligned, indel, nindel, type, score, pid, PairwiseAlignments, PairwiseAlignmentsSingleSubject, mismatch, nmatch, nmismatch, nedit, mismatchTable, mismatchSummary, coverage, compareStrings, lcprefix, lcsuffix, pmatchPattern, lcsubstr, pairwiseAlignment, stringDist, nchar, names, names<-, [[, narrow, consensusMatrix, consensusString, alphabetFrequency, as.list, rowmask, rowmask<-, colmask, colmask<-, maskGaps, maskednrow, maskedncol, maskeddim, consensusViews, needwunsQS, initialize, startIndex, endIndex, unlist, neditStartingAt, neditEndingAt, isMatchingStartingAt, isMatchingEndingAt, matchPattern, countPattern, vcountPattern, maskMotif, matchLRPatterns, trimLRPatterns, matchProbePair, maxWeights, minWeights, maxScore, minScore, PWM, matchPWM, countPWM, findPalindromes, findComplementedPalindromes, palindromeArmLength, complementedPalindromeArmLength, palindromeLeftArm, complementedPalindromeLeftArm, palindromeRightArm, complementedPalindromeRightArm, tb, tb.width, nnodes, hasAllFlinks, computeAllFlinks, head, tail, patternFrequency, PDict, matchPDict, countPDict, whichPDict, vmatchPDict, vcountPDict, vwhichPDict, ==, !=, duplicated, is.unsorted, order, sort, rank, toComplex, letter, substr, substring, letterFrequency, letterFrequencyInSlidingView, hasOnlyBaseLetters, uniqueLetters, oligonucleotideFrequency, nucleotideFrequencyAt, dinucleotideFrequencyTest, chartr, reverse, complement, reverseComplement, codons, translate, extractAt, replaceAt, replaceLetterAt, injectHardMask, unstrsplit, seqtype, seqtype<-, updateObject, append, relistToClass, splitAsListReturnedClass, union, intersect, setdiff, setequal, %in%, match, compare, as.data.frame, subseq, threebands, subseq<-, collapse, gaps, unmasked, maskedwidth, maskedratio, masks, masks<- ExportClasses: XStringPartialMatches, XStringQuality, PhredQuality, SolexaQuality, IlluminaQuality, QualityScaledXStringSet, QualityScaledBStringSet, QualityScaledDNAStringSet, QualityScaledRNAStringSet, QualityScaledAAStringSet, InDel, AlignedXStringSet0, AlignedXStringSet, QualityAlignedXStringSet, PairwiseAlignments, PairwiseAlignmentsSingleSubject, PairwiseAlignmentsSingleSubjectSummary, MultipleAlignment, DNAMultipleAlignment, RNAMultipleAlignment, AAMultipleAlignment, MIndex, ByPos_MIndex, BOC_SubjectString, BOC2_SubjectString, PreprocessedTB, Twobit, ACtree2, PDict3Parts, PDict, TB_PDict, MTB_PDict, Expanded_TB_PDict, XString, BString, DNAString, RNAString, AAString, XStringSet, BStringSet, DNAStringSet, RNAStringSet, AAStringSet, XStringViews, MaskedXString, MaskedBString, MaskedDNAString, MaskedRNAString, MaskedAAString, XStringSetList, BStringSetList, DNAStringSetList, RNAStringSetList, AAStringSetList Package: biosvd Exports: assayColorMap<-, contrast<-, featureColorMap<-, figure<-, filenames<-, negativeValues<-, palette<-, path<-, plots<-, prefix<-, whichAssays<-, whichEigenassays<-, whichEigenfeatures<-, whichFeatures<-, whichPolarAxes<-, apply, assayColorMap, assayMatrix, assaycorrelations, colorIdFeatures, contrast, eigenassays, eigenexpressions, eigenfeatures, entropy, excludeEigenfeatures, featureColorMap, featureMatrix, featurecorrelations, figure, filenames, fractions, matrix, negativeValues, palette, path, plots, prefix, signMatrix, whichAssays, whichEigenassays, whichEigenfeatures, whichFeatures, whichPolarAxes ExportMethods: report, project, plot, exclude, compute ExportClasses: EigensystemPlotParam, Eigensystem Package: biovizBase Exports: getBioColor, plotColorLegend, genBrewerBlindPalInfo, genDichromatPalInfo, genBlindPalInfo, colorBlindSafePal, blind.pal.info, brewer.pal.blind.info, dichromat.pal.blind.info, estimateCoverage, transformToCircle, transformToRectInCircle, transformToBarInCircle, transformToSegInCircle, transformToLinkInCircle, transformDfToGr, transformGRangesForEvenSpace, isIdeogram, isSimpleIdeogram, getIdeogram, containLetters, pileupAsGRanges, pileupGRangesAsVariantTable, GCcontent, showColor, isJunctionRead, isMatchedWithModel, flatGrl, getIdeoGR, getScale, getFormalNames, subsetArgsByFormals, parseArgsForAes, parseArgsForNonAes, strip_formula_dots, is_coord_truncate_gaps, is_coord_genome ExportMethods: addStepping, shrinkageFun, maxGap, splitByFacets, getGaps, getXScale, getYLab, getXLab, crunch, mold, transformToGenome, transformToDf Package: BiRewire Exports: birewire.analysis.undirected, birewire.rewire, birewire.analysis, birewire.rewire.bipartite, birewire.bipartite.from.incidence, birewire.similarity, birewire.rewire.bipartite.and.projections Package: birta Exports: birta, get_potential_swaps, limmaAnalysis, plotConvergence Package: BiSeq Exports: methLevel, methLevel<-, methReads, methReads<-, totalReads, totalReads<-, BSraw, BSrel, annotateGRanges, betaRegression, binomLikelihoodSmooth, clusterSites, clusterSitesToGR, compareTwoSamples, covBoxplots, covStatistics, estLocCor, filterByCov, filterBySharedRegions, findDMRs, globalTest, limitCov, logisticRegression, makeVariogram, plotBindingSites, plotMeth, plotMethMap, plotSmoothMeth, predictMeth, rawToRel, readBismark, smoothVariogram, summarizeRegions, testClusters, trimClusters, writeBED ExportMethods: combine ExportClasses: BSraw, BSrel Package: BitSeq Exports: parseAlignment, estimateExpression, estimateExpressionLegacy, estimateVBExpression, getMeanVariance, estimateHyperPar, estimateDE, getGeneExpression, getWithinGeneExpression, getDE, getExpression, loadSamples, writeSamples Package: blima Exports: chipArrayStatistics, log2TransformPositive, bacgroundCorrect, writeBackgroundImages, plotBackgroundImageBeforeCorrection, plotBackgroundImageAfterCorrection, nonPositiveCorrect, varianceBeadStabilise, quantileNormalize, doTTests, doProbeTTests, createSummarizedMatrix, backgroundChannelSubtract, selectedChannelTransform, xieBacgroundCorrect Package: BRAIN Exports: getAtomsFromSeq, useBRAIN, calculateIsotopicProbabilities, calculateAverageMass, calculateMonoisotopicMass, calculateNrPeaks Package: BrainStars Exports: getBrainStars, getBrainStarsFigure Package: bridge Exports: bridge.2samples, bridge.3samples Package: BridgeDbR Exports: getSystemCode, getOrganismCode, getBridgeNames, getDatabase, getMatchingSources, getFullName, getDataSource, loadDatabase, map Package: BSgenome Exports: newSNPlocs, BSgenome, MaskedBSgenome, installed.genomes, available.genomes, getBSgenome, installed.SNPs, available.SNPs, bsapply, GenomeData, GenomeDataList, referenceGenome, compatibleGenomes, snpcount, snplocs, snpid2loc, snpid2alleles, snpid2grange, sourceUrl, SNPlocs, SNPlocs_pkgname, SNPcount, mseqnames, masknames, injectSNPs, gdapply, gdReduce, forgeSeqlengthsFile, forgeSeqFiles, forgeMasksFiles, forgeBSgenomeDataPkg, forgeMaskedBSgenomeDataPkg ExportMethods: length, names, as.list, show, [[, $, score, seqinfo, seqinfo<-, seqnames, seqnames<-, organism, species, provider, providerVersion, releaseDate, releaseName, getSeq, matchPWM, countPWM, vmatchPattern, vcountPattern, referenceGenome, compatibleGenomes, snpcount, snplocs, snpid2loc, snpid2alleles, snpid2grange, sourceUrl, SNPlocs, SNPlocs_pkgname, SNPcount, mseqnames, masknames, injectSNPs, gdapply, gdReduce, forgeBSgenomeDataPkg ExportClasses: SNPlocs, InjectSNPsHandler, BSgenome, MaskedBSgenome, GenomeData, GenomeDataList, BSgenomeDataPkgSeed Package: bsseq Exports: BSseq, getMeth, getCoverage, getBSseq, getStats, collapseBSseq, orderBSseq, hasBeenSmoothed, chrSelectBSseq, BSmooth, BSmooth.tstat, dmrFinder, fisherTests, combineList, plotRegion, plotManyRegions, read.umtab, read.umtab2, read.bsmooth, read.bismark, poissonGoodnessOfFit, binomialGoodnessOfFit, data.frame2GRanges, BSseqTstat, assayNames ExportMethods: assays, [, show, seqnames, seqnames<-, seqlevels, seqlevels<-, seqlengths, seqlengths<-, start, start<-, end, end<-, width, width<-, strand, strand<-, granges, dim, nrow, ncol, sampleNames, sampleNames<-, pData, pData<-, findOverlaps, subsetByOverlaps, combine, updateObject ExportClasses: hasGRanges, BSseq, BSseqTstat, matrixOrNULL Package: BufferedMatrix ExportMethods: buffer.dim, is.ColMode, is.RowMode, RowMode, ColMode, set.buffer.dim, prefix, directory, filenames, duplicate, ewApply, pow, Max, Min, Sum, Var, Sd, rowMeans, rowSums, rowVars, rowSd, rowMax, rowMin, rowMedians, colMeans, colSums, colVars, colSd, colMax, colMin, colMedians, colRanges, colApply, rowApply, subBufferedMatrix, rownames, colnames, colnames<-, rownames<-, ReadOnlyMode, is.ReadOnlyMode, memory.usage, disk.usage, AddColumn, MoveStorageDirectory, coerce, [, show, as.matrix, ncol, nrow, mean ExportClasses: BufferedMatrix Package: BufferedMatrixMethods Exports: bg.correct.BufferedMatrix, normalize.BufferedMatrix.quantiles, BufferedMatrix.read.celfiles, BufferedMatrix.read.probematrix, BufferedMatrix.justRMA, BufferedMatrix.bg.correct.normalize.quantiles ExportMethods: median.polish.summarize Package: bumphunter Exports: bumphunter, bumphunterEngine, clusterMaker, boundedClusterMaker, dummyData, getSegments, loessByCluster, pointMatch, regionFinder, regionMatch, annotateNearest, runmedByCluster, smoother, matchGenes, locfitByCluster, known_transcripts ExportMethods: bumphunter Package: BUS Exports: BUS, pred.network, gene.similarity, gene.trait.similarity, gene.pvalue, gene.trait.pvalue Package: CAFE Exports: ProcessCels, chromosomeStats, bandStats, armStats, fisher.method, cliSubset, discontPlot, discontSmooth, facetPlot, guiSubset, rawPlot, slidPlot, slidSmooth Package: CAGEr Exports: genomeName, inputFiles, inputFilesType, sampleLabels, librarySizes, CTSScoordinates, CTSStagCount, CTSSnormalizedTpm, CTSSclusteringMethod, tagClusters, consensusClusters, consensusClustersTpm, expressionClasses ExportMethods: scoreShift, getShiftingPromoters, quantilePositions, normalizeTagCount, mergeSamples, show, getExpressionProfiles, extractExpressionClass, plotCorrelation, plotReverseCumulatives, exportCTSStoBedGraph, plotInterquantileWidth, plotExpressionProfiles, exportToBed, setColors, cumulativeCTSSdistribution, clusterCTSS, aggregateTagClusters, getCTSS, importPublicData ExportClasses: CAGEset Package: CALIB ExportMethods: show ExportClasses: RGList_CALIB, SpikeList, ParameterList Package: CAMERA Exports: annotate, annotateDiffreport, cleanParallel, combinexsAnnos, getIsotopeCluster, getpspectra, findKendrickMasses, findNeutralLoss, findNeutralLossSpecs, pspec2metfrag, pspec2metfusion, xsAnnotate ExportMethods: setDefaultLists, readLists, setDefaultParams, setParams, generateRules, calcCiS, calcCaS, calcIsotopes, calcPC, calcPC.lpc, calcPC.hcs, getAllPeakEICs, getPeaklist, plotPsSpectrum, plotEICs, show, findAdducts, groupDen, groupCorr, findIsotopes, groupFWHM ExportClasses: ruleSet, xsAnnotate Package: cancerclass Exports: validate, nvalidate, fit, loo, .First.lib, .initFoo, get.d, get.d2, ilogit, calc.roc, calc.auc, get.ntrain, prepare, filter, get.lm ExportMethods: plot3d, summary, plot, predict ExportClasses: validation, nvalidation, predictor, prediction Package: CancerMutationAnalysis Exports: cma.scores, cma.fdr, cma.set.stat, cma.set.sim, extract.sims.method, combine.sims ExportMethods: show ExportClasses: SetMethodsSims Package: casper Exports: asymmetryCheck, calcDenovo, calcExp, casperDesign, createDenovoGenome, denovoExpr, getDistrs, getIsland, genePlot, getRoc, mergeBatches, mergeExp, modelPrior, pathCounts, plotPriorAS, posprob, probNonEquiv, procBam, procGenome, pvalTreat, qqnormGenomeWide, quantileNorm, relativeExpr, relexprByGene, rmShortInserts, simMAE, simMultSamples, simReads, transcripts, variants, variants<-, getReads, getNreads, getChr, getIsland, subsetGenome, txLength, wrapKnown, simMAE, simMAEcheck ExportMethods: plot, lines, coef, [, [[, as.list ExportClasses: annotatedGenome, simulatedSamples, pathCounts, procBam Package: Category Exports: .doHyperGTest, applyByCategory, cateGOry, cb_children, cb_contingency, cb_parse_band_Hs, cb_parse_band_Mm, cb_sigBands, cb_test, ChrBandTreeFromGraph, DatPkgFactory, exampleLevels, findAMstats, geneIds, geneIds<-, getPathNames, gseattperm, hyperg, makeChrBandGraph, makeChrBandInciMat, makeChrBandGSC, makeEBcontr, NewChrBandTree, MAPAmat, ontology, probes2MAP, probes2Path, ttperm, GSEAGOHyperGParams, GSEAKEGGHyperGParams ExportMethods: hyperGTest, linearMTest, universeBuilder, categoryToEntrezBuilder, categoryName, makeValidParams, chrGraph, pvalues, effectSize, geneCounts, universeCounts, universeMappedCount, geneMappedCount, annotation, annotation<-, DatPkgFactory, geneIds, geneIds<-, geneIdsByCategory, geneIdUniverse, testName, pvalueCutoff, pvalueCutoff<-, testDirection, testDirection<-, description, universeGeneIds, ontology, ontology<-, conditional, conditional<-, oddsRatios, expectedCounts, htmlReport, sigCategories, ID2GO, ID2EntrezID, GO2AllProbes, ID2KEGG, KEGG2AllProbes, initialize, show, summary, allGeneIds, childrenOf, level2nodes, lgeneIds, parentOf, treeLevels ExportClasses: DatPkg, AffyDatPkg, YeastDatPkg, Org.XX.egDatPkg, HyperGParams, GOHyperGParams, KEGGHyperGParams, PFAMHyperGParams, ChrMapHyperGParams, HyperGResultBase, HyperGResult, ChrMapHyperGResult, ChrBandTree, KEGGHyperGResult, PFAMHyperGResult, LinearMParams, ChrMapLinearMParams, LinearMResultBase, LinearMResult, ChrMapLinearMResult Package: categoryCompare ExportMethods: fdr, fdr<-, hyperGTestCC, fdrvalues, listNames, compareNames, compareNames<-, compareIndx, compareColors, compareColors<-, ccType, ccType<-, organism, pvalueType, pvalueType<-, outType, outType<-, minCount, minCount<-, ccEnrich, ccCompare, mainGraph, mainTable, allAnnotation, ccOutCyt, annotation, ontology, geneAnnMapping, graphType, graphType<-, sigID, mergeLists, cwReload, cytOutNodes, cytOutData, resetColors, breakEdges, pvalueCutoff, pvalueCutoff<- ExportClasses: HyperGParamsCC, GOHyperGParamsCC, KEGGHyperGParamsCC, HyperGResultCC, GOHyperGResultCC, KEGGHyperGResultCC, ccOptions, ccGeneList, ccEnrichResult, GOccEnrichResult, KEGGccEnrichResult, ccEnrichCollection, ccCompareResult, ccCompareCollection, ccSigList, GENccEnrichResult, mergedData Package: ccrepe Exports: ccrepe, nc.score Package: cellGrowth Exports: bandwidthCV, baranyi, fitCellGrowth, fitCellGrowths, getRowColumn, getWellIdsTecan, gompertz, guessCellGrowthParams, logistic, plot.cellGrowthFit, plot.well, plotPlate, readGenios, readYeastGrower, rosso, standardWellId, wellDataFrame Package: cellHTS Exports: ROC, annotate, Bscore, configure, getEnVisionRawData, getEnVisionCrosstalkCorrectedData, getLibraryPlate, getMatrix, imageScreen, normalizeChannels, normalizePlates, oneRowPerId, plotSpatialEffects, plotPlateLibrary, readPlateData, screenMatch, summarizeChannels, summarizeReplicates, write.tabdel, writeReport, writeTab Package: cellHTS2 Exports: oneRowPerId, Bscore, buildCellHTS2, configurationAsScreenPlot, convertOldCellHTS, convertWellCoordinates, getEnVisionRawData, getEnVisionCrosstalkCorrectedData, getDynamicRange, getMeasureRepAgreement, getTopTable, getSettings, getZfactor, gseaModule, imageScreen, normalizePlates, plotSpatialEffects, readPlateList, readHTAnalystData, rsa, scores2calls, scoreReplicates, setSettings, spatialNormalization, summarizeChannels, summarizeReplicates, templateDescriptionFile, updateCellHTS, writeReport, write.tabdel ExportMethods: annotate, batch, batch<-, compare2cellHTS, coerce, configure, Data, Data<-, geneAnno, initialize, intensityFiles, lines, meanSdPlot, name, name<-, nbatch, pdim, plate, plateConf, plateEffects, plateList, plot, position, ROC, screenDesc, screenLog, show, state, well, wellAnno, writeTab ExportClasses: cellHTS, ROC Package: CellNOptR Exports: buildBitString, checkSignals, exhaustive, CNOdata, CNORwrap, CNORbool, CNOlist, compressModel, computeScoreT1, computeScoreTN, cSimulator, cutAndPlot, cutAndPlotResultsT1, cutAndPlotResultsTN, cutCNOlist, cutNONC, cutSimList, cutModel, defaultParameters, expandGates, findNONC, gaBinaryT1, gaBinaryT2, gaBinaryTN, graph2sif, getFit, indexFinder, mapBack, makeCNOlist, model2sif, model2igraph, normaliseCNOlist, plotCNOlist, plotCNOlist2, plotCNOlistLarge, plotCNOlistLargePDF, plotCNOlistPDF, plotFit, plotOptimResults, plotOptimResultsPan, plotOptimResultsPDF, prep4sim, prep4Sim, preprocessing, randomizeCNOlist, readSBMLQual, readMIDAS, readSIF, readSif, residualError, sif2graph, simulateT1, simulateTN, simulatorT0, simulatorT1, simulatorTN, writeDot, writeMIDAS, writeSIF, writeNetwork, writeReport, writeScaffold, plotModel ExportMethods: setSignals<-, getCues, getSignals, getStimuli, getInhibitors, getVariances, getTimepoints, plot, randomize, length, compatCNOlist ExportClasses: CNOlist Package: CexoR Exports: cexor Package: CGEN Exports: snp.scan.logistic, snp.logistic, recode.geno, getSummary, getWaldTest, QQ.plot, chromosome.plot, snp.effects, getMatchedSets, snp.matched, printEffects, additive.test, snp.effects.plot, GxE.scan, score.test, GxE.scan.combine, GxE.scan.partition Package: CGHbase Exports: make_cghRaw ExportMethods: initialize, plot.cghRaw, plot.cghSeg, plot.cghCall, plot.cghRegions, frequencyPlot, chromosomes, bpstart, bpend, avedist, nclone, copynumber, segmented, calls, regions, probloss, probnorm, probgain, probamp ExportClasses: cghRaw, cghSeg, cghCall, cghRegions Package: CGHcall ExportMethods: initialize ExportClasses: cghRaw, cghSeg, cghCall Package: cghMCR Exports: cghMCR, plot.DNAcopy, MCR, mergeMCRProbes, SGOL ExportMethods: gol, plot ExportClasses: cghMCR, SGOL Package: ChAMP Exports: champ.process, champ.load, champ.norm, champ.CNA, champ.SVD, champ.lasso, champ.MVP, champ.runCombat Package: charm Exports: bgAdjust, countGC, cpgdensity, dmrFdr, dmrFinder, dmrPlot, regionPlot, getControlIndex, maxDensity, pmQuality, methPercent, methp, normalizeBetweenSamples, normalizeWithinSamples, plotDensity, qcReport, readCharm, spatialAdjust, validatePd, controlQC, cmdsplot, dmrFind, qval, plotDMRs, plotRegions, clusterMaker, regionMatch, pmindex, bgindex Package: ChemmineOB Exports: convertFormat, convertFormatFile, prop_OB, fingerprint_OB, smartsSearch_OB, exactMass_OB, canonicalNumbering_OB, forEachMol Package: ChemmineR Exports: atomprop, pubchemFPencoding, read.SDFstr, read.SDFset, read.SMIset, sdfStream, read.AP, read.SDFindex, write.SDF, write.SMI, write.SDFsplit, validSDF, makeUnique, atomcountMA, MW, MF, datablock2ma, splitNumChar, grepSDFset, conMA, bonds, groups, rings, atomsubset, SDFset, maximallyDissimilar, plotStruc, SDF2apcmp, sdf2ap, apset2descdb, desc2fp, cmp.search, cmp.similarity, cmp.parse, cmp.parse1, sdf.subset, db.explain, cluster.sizestat, cmp.duplicated, sdf.visualize, db.subset, smiles2sdf, sdf2smiles, propOB, fingerprintOB, regenerateCoords, smartsSearchOB, exactMassOB, generate3DCoords, canonicalize, canonicalNumbering, fp2bit, fpSim, getIds, searchString, searchSim, sdf2smiles, smiles2sdf, cmp.cluster, jarvisPatrick, cluster.visualize, nearestNeighbors, trimNeighbors, fromNNMatrix, byCluster, initDb, loadSdf, loadSmiles, getCompounds, findCompounds, getCompoundNames, findCompoundsByName, addNewFeatures, listFeatures, jarvisPatrick_c, genAPDescriptors, addDescriptorType, setPriorities, randomPriorities, forestSizePriorities, getAllCompoundIds, getCompoundFeatures, bufferLines, bufferResultSet, parBatchByIndex, batchByIndex, selectInBatches, dbTransaction, DUD, DrugBank, status, browseJob, result, listCMTools, toolDetails, launchCMTool ExportMethods: sdfstr2list, sdf2list, sdf2str, SDFset2list, SDFset2SDF, sdfstr2list<-, SDFset2SDF<-, cid<-, header<-, atomblock<-, bondblock<-, datablock<-, [, [[, [<-, [[<-, coerce, show, length, c, plot, as.matrix, header, atomblock, bondblock, datablock, view, cid, sdfid, atomcount, datablocktag, obmol, fold, foldCount, fptype, numBits, ap ExportClasses: SDFstr, SDF, SDFset, SMI, SMIset, AP, APset, FP, FPset, jobToken Package: chimera Exports: plotCoverage, is.fSet Package: chipenrich Exports: chipenrich, plot_spline_length, plot_dist_to_tss, plot_gene_coverage, plot_expected_peaks Package: ChIPpeakAnno Exports: getAnnotation, annotatePeakInBatch, assignChromosomeRegion, getAllPeakSequence, write2FASTA, getEnrichedGO, getEnrichedPATH, getUniqueGOidCount, hyperGtest, convert2EntrezID, addAncestors, BED2RangedData, GFF2RangedData, makeVennDiagram, findOverlappingPeaks, peaksNearBDP, summarizePatternInPeaks, countPatternInSeqs, translatePattern, addGeneIDs, condenseMatrixByColnames Package: ChIPQC Exports: ChIPQCsample, ChIPQC ExportMethods: averagepeaksignal, coveragehistogram, crosscoverage, flagtagcounts, fragmentlength, FragmentLengthCrossCoverage, Normalisedaveragepeaksignal, peaks, ReadLengthCrossCoverage, RelativeCrossCoverage, show, ssd, readlength, plotCC, plotPeakProfile, plotFrip, plotFribl, plotRap, plotCoverageHist, plotRegi, frip, rip, ribl, regi, mapped, QCmetrics, QCsample, QCcontrol, QCmetadata, QCannotation, QCdba, reads, duplicates, duplicateRate, plotCorHeatmap, plotPrincomp, ChIPQCreport, plotSSD ExportClasses: ChIPQCsample, ChIPQCexperiment Package: ChIPseeker Exports: annotatePeak, as.GRanges, covplot, downloadGEObedFiles, downloadGSMbedFiles, enrichAnnoOverlap, enrichPeakOverlap, getGEOInfo, getGEOgenomeVersion, getGEOspecies, getPromoters, getSampleFiles, getTagMatrix, overlap, peakHeatmap, plotAnnoBar, plotAnnoPie, plotAnnoPie.csAnno, plotAvgProf, plotAvgProf2, plotChrCov, plotDistToTSS, readPeakFile, shuffle, tagHeatmap, vennpie, vennplot, vennplot.peakfile ExportMethods: vennpie, show, plotDistToTSS, plotAnnoPie, plotAnnoBar ExportClasses: csAnno Package: chipseq Exports: diffPeakSummary, laneSubsample, chipseqFilter, islandDepthPlot, coverageplot, sparse.density, basesCovered, densityCorr, estimate.mean.fraglen, subsetSummary, peakCutoff, peakSummary ExportMethods: estimate.mean.fraglen Package: ChIPseqR ExportMethods: strandPileup, callBindingSites, [[, [, $, names, [[<-, [<-, $<-, names<-, lapply, sapply, as.data.frame, head, tail, min, max, range, nreads, chrLength, score, pvalue, peaks, cutoff, cutoff<-, nullDist, nullDist<-, plot, compress, decompress ExportClasses: ReadCounts, BindScore, RLEReadCounts, RLEBindScore Package: ChIPXpress Exports: ChIPXpress, buildDatabase, cleanDatabase Package: chopsticks Exports: epsout.ld.snp, glm.test.control, ibs.stats, ibsCount, ibsDist, ld.snp, ld.with, niceprint, pair.result.ld.snp, plot.snp.dprime, print.snp.dprime, qq.chisq, read.HapMap.data, read.pedfile.info, read.snps.chiamo, read.snps.long, read.snps.long.old, read.snps.pedfile, read.wtccc.signals, row.summary, single.snp.tests, snp.cbind, snp.rbind, snp.cor, snp.lhs.tests, snp.post, snp.pre, snp.rhs.tests, write.snp.matrix, xxt, convert.snpMatrix, convert.snpMatrix.dir ExportMethods: cbind2, is.na, ld.with, rbind2, show, summary, [, [<-, coerce, initialize ExportClasses: snp.matrix, X.snp.matrix, snp, X.snp, snp.dprime Package: chroGPS Exports: adjustPeaks, distGPS, procrustesAdj, clusGPS, mergeClusters, profileClusters, mds, geneSetGPS, domainDist, addVar, uniqueCount, contour2dDP, plotContour, getURL, gff2RDList, boostMDS ExportMethods: distGPS, procrustesAdj, adjustPeaks, mds, clusGPS, mergeClusters, geneSetGPS, plot, gps2xgmml, clusNames, tabClusters, clusterID, getR2, getStress, getPoints, is.adj, as.matrix ExportClasses: mds, distGPS, clusGPS, hclust Package: ChromHeatMap Exports: plotChrMap, makeChrStrandData, grabChrMapProbes, makeRangedDataList, createChrMatrix, chrHeatMap, drawMapDendro ExportMethods: chrNames ExportClasses: ChrStrandData, ChrStrandMatrix, ChrMapPlot Package: cisPath Exports: cisPath, networkView, easyEditor, getMappingFile, formatPINAPPI, formatSIFfile, formatSTRINGPPI, formatiRefIndex, combinePPI Package: cleanUpdTSeq Exports: BED2GRangesSeq, getUpstreamSequence, getDownstreamSequence, buildFeatureVector, predictTestSet Package: cleaver ExportMethods: cleave, cleavageRanges, cleavageSites Package: clippda Exports: sampleClusteredData, negativeIntensitiesCorrection ExportMethods: show ExportClasses: aclinicalProteomicsData Package: clipper Exports: cliqueVarianceTest, cliqueMeanTest, cliqueMixedTest, getGraphEntryGenes, getJunctionTreePaths, pathQ, clipper, prunePaths, easyClip, plotInCytoscape, nameCliques, deleteEdge, easyLook, clipperAllRoots, cliquePairedTest Package: Clomial Exports: Clomial, choose.best, Clomial.generate.data, Clomial.iterate, compute.bic, Clomial.likelihood, compute.errors Package: Clonality Exports: ave.adj.probes, chromosomePlots, clonality.analysis, genomewidePlots, histogramPlot, LOHclonality, splitChromosomes, ECMtesting, LRtesting3or4tumors Package: clst Exports: partition, findThreshold, plotDistances, plotMutinfo, classifier, classify, classifyIter, printClst, pull, pullTab, scaleDistPlot Package: clstutils Exports: classifyPlacements, treeDists, maxDists, findOutliers, refpkgContents, taxonomyFromRefpkg, prettyTree Package: clusterProfiler Exports: Gff2GeneTable, buildGOmap, cnetplot, compareCluster, enrichGO, enrichKEGG, enrichMap, groupGO, gseGO, gseKEGG, gseaplot, plot ExportClasses: groupGOResult, compareClusterResult Package: clusterStab ExportMethods: ecdf, hist, benhur, clusterComp ExportClasses: BenHur, ClusterComp Package: CMA Exports: GenerateLearningsets, ttest, welchtest, wilcoxtest, ftest, kruskaltest, limmatest, golubcrit, rfe ExportMethods: show, summary, toplist, plot, best, boxplot, ftable, roc, obsinfo, GeneSelection, tune, classification, join, evaluation, compare, Planarplot, ldaCMA, svmCMA, shrinkldaCMA, scdaCMA, rfCMA, qdaCMA, pnnCMA, pls_rfCMA, pls_lrCMA, pls_ldaCMA, plrCMA, pknnCMA, knnCMA, nnetCMA, LassoCMA, ElasticNetCMA, compBoostCMA, gbmCMA, dldaCMA, fdaCMA, flexdaCMA, prediction, weighted.mcr, wmc ExportClasses: learningsets, cloutput, varseloutput, clvarseloutput, genesel, evaloutput, predoutput, tuningresult Package: cn.farms Exports: cn.farms, cnLibrary, combineData, createAnnotation, createMatrix, distributionDistance, dnaCopySf, fragLengCorr, mlSummarization, normalizeAverage, normalizeCels, normalizeNpData, normalizeSequenceEffect, plotDendrogram, plotDensity, plotEvalIc, plotRegions, plotSmoothScatter, plotViolines, slSummarization, sparseFarmsC, summarizeFarmsExact, summarizeFarmsExact2, summarizeFarmsExact3, summarizeFarmsGaussian, summarizeFarmsMethods, summarizeFarmsStatistics, summarizeFarmsVariational, summarizeWindowBps, summarizeWindowMethods, summarizeWindowStd Package: cn.mops Exports: cn.mops, exomecn.mops, getReadCountsFromBAM, getSegmentReadCountsFromBAM, haplocn.mops, normalizeChromosomes, normalizeGenome, referencecn.mops, segment, singlecn.mops ExportMethods: show, segplot, segmentation, sampleNames, posteriorProbs, plot, params, normalizedData, makeRobustCNVR, localAssessments, integerCopyNumber, iniCall, individualCall, gr, cnvs, cnvr, calcIntegerCopyNumbers, calcFractionalCopyNumbers ExportClasses: CNVDetectionResult Package: CNAnorm Exports: dataFrame2object, CNAnormWorkflow ExportMethods: gcNorm, chrs, arms, pos, chrs<-, pos<-, ratio, ratio.n, ratio.s, ratio.s.n, segMean, segMean.n, addSmooth, addDNACopy, plotPeaks, plotGenome, peakPloidy, sugg.ploidy, sugg.peaks, valid.ploidy, valid.peaks, validation, exportTable, discreteNorm ExportClasses: CNAnorm, InData, DerivData, Params Package: CNEr Exports: reverseCigar, binFromCoordRange, binRangesFromCoordRange, binRestrictionString, readCNERangesFromSQLite, fetchChromSizes, Axt, CNE, readBed, readAxt, axtInfo, writeAxt, ceScan, cneMerge, blatCNE, ceScanOneStep, queryCNEData, CNEDensity ExportMethods: targetRanges, queryRanges, targetSeqs, querySeqs, symCount, subAxt, assembly1, assembly2, CNE1, CNE2, thresholds, CNEMerged, CNERepeatsFiltered, saveCNEToSQLite, CNEDensity, [, c, length, score, nchar ExportClasses: Axt, CNE Package: CNORdt Exports: simulatorDT, getFitDT, gaBinaryDT, cutAndPlotResultsDT, computeScoreDT, convert2array Package: CNORfeeder Exports: Binference, gaBinaryT1W, linksRanking, makeBTables, mapBTables2model, mapDDN2model, MIinference, weighting Package: CNORfuzzy Exports: CNORwrapFuzzy, computeScoreFuzzy, compileMultiRes, defaultParametersFuzzy, gaDiscreteT1, getRefinedModel, interpretDiscreteGA, plotMeanFuzzyFit, prep4simFuzzy, reduceFuzzy, simFuzzyT1, writeFuzzyNetwork Package: CNORode Exports: createLBodeContPars, defaultParametersGA, defaultParametersSSm, getLBodeContObjFunction, getLBodeDataSim, getLBodeMINLPObjFunction, getLBodeModelSim, getLBodeSimFunction, getStates, incidence2Adjacency, minlpLBodeSSm, parEstimationLBodeGA, parEstimationLBode, parEstimationLBodeSSm, plotLBodeFitness, plotLBodeModelSim, simdata2cnolist, simulate Package: CNTools Exports: diffBy, CNSeg ExportMethods: getRS, segBy, rs, genefilter, getCor, rs<-, getDist, segList<-, show, segList, madFilter ExportClasses: CNSeg, RS Package: cnvGSA Exports: cnvGSAFisher, cnvGSAexportBurdenStats, getCnvGenes, readGMT, readGVF, readParamsRFile, CnvGSAInput, cnvData, cnvData<-, gsData, gsData<-, geneData, geneData<-, params, params<-, burdenSample, burdenGs, enrRes ExportMethods: cnvData, cnvData<-, gsData, gsData<-, geneData, geneData<-, params, params<-, burdenSample, burdenGs, enrRes ExportClasses: CnvGSAInput, CnvGSAOutput Package: CNVrd2 Exports: calculateLDSNPandCNV, groupBayesianCNVs ExportMethods: countReadInWindow, emnormalCNV, groupCNVs, plotCNVrd2, searchGroupCNVs, segmentSamples, segmentSamplesUsingPopInformation, identifyPolymorphicRegion, plotPolymorphicRegion ExportClasses: clusteringCNVs, CNVrd2, numericOrNULL Package: CNVtools Exports: CNVtest.select.model, CNVtest.binary, CNVtest.binary.T, CNVtest.qt, CNVtest.qt.T, apply.pca, apply.ldf, cnv.plot, qt.plot, getQualityScore, compact.data.frame, get.model.spec, CNV.fitModel Package: cobindR Exports: read.transfac.pfm, generate.background, cobindr, seqObj, cobindRConfiguration ExportMethods: detrending, find.pairs, get.bindingsite.ranges, plot.detrending, plot.gc, plot.pairdistance, plot.positionprofile, plot.positions, plot.positions.simple, plot.tfbs.heatmap, plot.tfbs.venndiagram, plot.tfbslogo, predicted2pwm, rtfbs, search.gadem, search.pwm, testCpG, write.bindingsites, write.bindingsites.table, get.pairs, write.sequences, get.significant.pairs, uid, name, sequences, bg_sequences, desc, configuration, pfm, binding_sites, bg_binding_sites, pairs, bg_pairs, pairs_of_interest, species, location, comment, sequence, experiment_description, id, sequence_source, sequence_origin, sequence_type, bg_sequence_source, bg_sequence_type, bg_sequence_origin, downstream, upstream, max_distance, pfm_path, threshold, fdrThreshold, path, mart, pseudocount, pValue ExportClasses: cobindr, configuration, SeqObj Package: CoCiteStats Exports: actorAdjTable, gene.geneslist.sig, gene.geneslist.statistic, gene.gene.statistic, paperLen, twowayTable, twTStats Package: codelink Exports: readCodelink, writeCodelink, reportCodelink, plotMA, plotCorrelation, plotDensities, plotCV, imageCodelink, bkgdCorrect, normalize, mergeArray, createWeights, arrayNew, selCV, cutCV, fc2Cond, na2false, logCodelink, readCodelinkSet, Codelink2CodelinkSet ExportMethods: [, show, summary, summaryFlag, annotation, codCorrect, codNormalize, codPreprocess, probeNames, probeTypes, getSNR, getInt, getBkg, getInfo, getWeight, getFlag, meanSNR, codPlot, exprs, chipDevice, filterSNR, codUniverse, writeCluster, writeCodelink, averageProbes ExportClasses: Codelink, CodelinkSet, CodelinkSetUnique Package: CoGAPS Exports: CoGAPS, binaryA, calcCoGAPSStat, computeGeneGSProb, gapsMapRun, gapsRun, plotAtoms, plotDiag, plotGAPS, plotP, plotSmoothPatterns, reorderByPatternMatch, residuals Package: coGPS Exports: PCOPA, PatientSpecificGeneList, PlotTopPCOPA, plotCOPA, permCOPA Package: COHCAP Exports: COHCAP.annotate, COHCAP.qc, COHCAP.site, COHCAP.avg.by.site, COHCAP.avg.by.island, COHCAP.integrate.avg.by.site, COHCAP.integrate.avg.by.island, COHCAP.BSSeq.preprocess Package: COMPASS Exports: COMPASSDescription<-, metadata<-, COMPASS, COMPASSContainer, COMPASSContainerFromGatingSet, COMPASSDescription, CellCounts, Combinations, FunctionalityScore, GetThresholdedIntensities, PolyfunctionalityScore, Posterior, PosteriorDiff, PosteriorLogDiff, PosteriorPs, PosteriorPu, TotalCellCounts, UniqueCombinations, categories, markers, metadata, pheatmap, plot2, shinyCOMPASS, shinyCOMPASSDeps, transpose_list Package: compcodeR Exports: DESeq.GLM.createRmd, DESeq.nbinom.createRmd, DESeq2.createRmd, DSS.createRmd, EBSeq.createRmd, NBPSeq.createRmd, NOISeq.prenorm.createRmd, SAMseq.createRmd, TCC.createRmd, baySeq.createRmd, checkDataObject, checkTableConsistency, check_compData, check_compData_results, compData, convertListTocompData, convertcompDataToList, edgeR.GLM.createRmd, edgeR.exact.createRmd, generateCodeHTMLs, generateSyntheticData, listcreateRmd, logcpm.limma.createRmd, runComparison, runComparisonGUI, runDiffExp, sqrtcpm.limma.createRmd, summarizeSyntheticDataSet, ttest.createRmd, voom.limma.createRmd, voom.ttest.createRmd, vst.limma.createRmd, vst.ttest.createRmd ExportClasses: compData Package: compEpiTools ExportMethods: GRangesInPromoters, GRannotate, GRbaseCoverage, GRcoverage, GRcoverageInbins, GRcoverageSummit, GRmidpoint, countOverlapsInBins, distanceFromTSS, enhancers, featuresLength, getPromoterClass, GRanges2ucsc, GRannotateSimple, GRenrichment, GRsetwidth, makeGtfFromDb, matchEnhancers Package: CompGO Exports: annotateBedFromDb, getFnAnot_genome, zTransformDirectory, doZtrans.single, slidingJaccard, plotZScores, plotPairwise, plotTwoGODags, plotZRankedDAG, compareZscores, viewKegg, plotInteractive, PCAplot, plotDendrogram Package: ConsensusClusterPlus Exports: ConsensusClusterPlus, calcICL Package: copa Exports: copa, plotCopa, copaPerm, tableCopa, scatterPlotCopa, summaryCopa Package: COPDSexualDimorphism Exports: sdcd, sdcd.core, sdcd.vmr, do.sdcd.boxplot, my.smart.plot Package: copynumber Exports: winsorize, multipcf, pcf, aspcf, plotChrom, plotGenome, plotSample, plotAllele, plotFreq, plotHeatmap, plotGamma, plotAberration, imputeMissing, subsetData, subsetSegments, selectSegments, plotCircle, callAberrations, interpolate.pcf, pcfPlain, getGRangesFormat Package: CopyNumber450k Exports: CNV450kSet, getSummary, getSegments, findCNV, intersectCNV, subgroupDifference, dropSNPprobes, segmentize, computeSignificance, plotSample, plotDensity, plotPCA, write.csv ExportClasses: CNV450kSet Package: CoRegNet Exports: discretizeExpressionData, coregnet, hLICORN, masterRegulator, display ExportMethods: print, show, length, dim, summary, regulatorInfluence, addEvidences, coregulators, coerce, regulators, targets, activators, repressors, coregnetToList, coregnetToDataframe, addCooperativeEvidences, refine ExportClasses: coregnet Package: Cormotif Exports: cormotiffit, cormotiffitall, cormotiffitfull, cormotiffitsep, generank, plotIC, plotMotif Package: CorMut Exports: seqFormat, kaksCodon, kaksAA, ckaksCodon, ckaksAA, miCodon, miAA, jiAA, biCkaksCodon, biCkaksAA, biMICodon, biMIAA, biJIAA, seq_num.CorMut, kaks.CorMut, lod.CorMut, q.CorMut, ka.CorMut, ks.CorMut, mi.CorMut, p.value.CorMut, ckaks.CorMut, method.CorMut, positiveSite01.CorMut, positiveSite02.CorMut, state_1.CorMut, statistic_1.CorMut, state_2.CorMut, statistic_2.CorMut ExportMethods: filterSites, plot, biCompare ExportClasses: kaksCodon, kaksAA, ckaks, MI, biCkaksCodon, biCkaksAA, biMICodon, biMIAA, biJIAA Package: coRNAi Exports: cellHTS2df, df2lmFit, SDplot, MAplot, rlmmain, WithinScreenPlot, BetweenScreenPlot, updateDf, InteractLevelPlot, BoxPlotShorth, MainFitPlot, df2array, lmmain, estmodel, weightDf, PlotHeatmap, df2fitmatrix, interactiontable, tt2matrix, cortestmatrices, data2graph, Pplot Package: CORREP Exports: cor.balance, cor.bootci, cor.LRtest, cor.LRtest.std, cor.unbalance, permutest Package: cosmiq Exports: combine_spectra, create_datamatrix, peakdetection, retention_time, cosmiq, eicmatrix, quantify_combined Package: CoverageView Exports: export.wig, write.profile ExportMethods: cov.interval, cov.matrix, draw.heatmap, draw.profile, genome.covplot.cumdepth, genome.covplot.depth ExportClasses: CoverageBamFile, CoverageBigWigFile Package: cqn Exports: cqn, cqn.fixedlength, cqnplot Package: CRImage Exports: labelCells, SauvolaThreshold, plotCorrectedCN, correctCopyNumber, calculateOtsu, convertLABToRGB, convertRGBToLAB, convertHSVToRGB, convertRGBToHSV, colorCorrection, calculateMeanStdTarget, createBinaryImage, segmentImage, createClassifier, classifyCells, calculateCellularity, processAperio Package: CRISPRseek Exports: offTargetAnalysis, filterOffTarget, filtergRNAs, findgRNAs, searchHits, writeHits, translatePattern, getOfftargetScore, buildFeatureVectorForScoring, compare2Sequences, calculategRNAEfficiency Package: crlmm Exports: crlmm, crlmmIllumina, crlmmIlluminaV2, constructAffyCNSet, genotype, genotypeAffy, readIdatFiles, readGenCallOutput, snprma, snprma2, cnrmaAffy, snprmaAffy, crlmm2, genotype2, genotypeLD, genotypeAffy, genotype.Illumina, crlmmCopynumber2, crlmmCopynumberLD, crlmmCopynumber, genotypes, totalCopynumber, rawCopynumber, xyplot, ABpanel, validCEL, celDates, validCdfNames ExportMethods: CA, CB, A, B, corr, nuA, nuB, phiA, phiB, predictionRegion, posteriorProbability, tau2, Ns, medians, mads, xyplot, calculateRBaf, OligoSetList, BafLrrSetList ExportClasses: PredictionRegion Package: csaw Exports: csawUsersGuide, correlateReads, getPETSizes, regionCounts, windowCounts, normalizeCounts, combineTests, getBestTest, mergeWindows, detailRanges, extractReads, readParam ExportMethods: show, $, reform, normalize, asDGEList ExportClasses: readParam Package: CSSP Exports: bindcount, bindcount.chr, callpeak, createBinData, cssp.fit, cssp.power, cssp.sim, fit.freq, pBBT, peakcount, peakcount.chr, qBBT, readBinFile, tag2bin, tag2bin.chr ExportClasses: CSSPFit, BinData Package: ctc Exports: hc2Newick, hclust2treeview, r2cdt, r2atr, r2gtr, r2cluster, r2xcluster, read.eisen, xcluster, xcluster2r Package: cummeRbund Exports: readCufflinks, JSdist, JSdistVec, JSdistFromP, shannon.entropy, makeprobs, makeprobsvec, csClusterPlot ExportMethods: runInfo, varModel, annotation, genes, isoforms, TSS, CDS, promoters, splicing, relCDS, fpkm, repFpkm, count, distValues, csDensity, csScatter, csVolcano, csBoxplot, csHeatmap, csFoldChangeHeatmap, csDistHeat, csCluster, csDendro, MAplot, dispersionPlot, csSpecificity, fpkmMatrix, repFpkmMatrix, countMatrix, repCountMatrix, diffData, diffTable, features, featureNames, samples, replicates, expressionPlot, expressionBarplot, getGene, getGenes, getFeatures, getGeneId, findGene, getSig, getSigTable, addFeatures, getLevels, getRepLevels, findSimilar, makeRnk, genePlot, makeGeneRegionTrack, DB, sigMatrix, csScatterMatrix, csVolcanoMatrix, MDSplot, PCAplot, fpkmSCVPlot, csNMF, conditions, csPie ExportClasses: CuffSet, CuffData, CuffDist, CuffFeature, CuffFeatureSet, CuffGene, CuffGeneSet Package: customProDB Exports: PrepareAnnotationEnsembl, PrepareAnnotationRefseq, easyRun, easyRun_mul, calculateRPKM, Outputproseq, InputVcf, Varlocation, Positionincoding, aaVariation, OutputVarproseq, OutputVarproseq_single, Outputaberrant, Bed2Range, JunctionType, OutputNovelJun, OutputsharedPro, Multiple_VCF, SharedJunc Package: cycle Exports: ar1analysis, backgroundData, fdrfourier, fourierscore Package: daMA Exports: analyseMA, cinfo, cinfoB.AB, cmat, cmatB.AB, core, designMA, designs.basic, designs.composite Package: DART Exports: DoDART, BuildRN, EvalConsNet, PruneNet, PredActScore Package: DASiR Exports: getDasFeature, setDasServer, getDasServer, getDasSource, getDasDsn, getDasEntries, getDasTypes, getDasStructure, plotFeatures, getDasSequence Package: DBChIP Exports: DBChIP, read.binding.site.list, site.merge, load.data, get.site.count, test.diff.binding, report.peak, plotPeak Package: ddCt Exports: barploterrbar, ddCtAbsolute, elist, errBarchart, SDMFrame, CSVFrame, readSDM, ColMap, replaceVectorByEquality, write.htmltable, writeSimpleTabCsv, getDir ExportMethods: coreData, coreData<-, rightCensoring, fileNames, sampleNames, sampleNames<-, uniqueDetectorNames, uniqueDetectorNames<-, uniqueSampleNames, uniqueSampleNames<-, detectorNames<-, detectorNames, replaceDetector, replaceSample, removeDetector, removeSample, removeNTC, level, levelErr, Ct, Ct<-, CtErr, dCt, dCtErr, ddCt, ddCtErr, numberCt, numberNA, ddCtExpression, errBarchart, InputFrame, elistWrite ExportClasses: ddCtExpression, InputFrame, InputReader, SDMReader, CSVReader, ColMap Package: ddgraph Exports: calcDependence, mcX2Test, mcMITest, mcX2TestB50k, combinationsTest, blockingVariables, blockingNodes, activePaths, readFurlongData, makeDDDataSet, is.binary, convertToFactor, ncpc, plotBNLearn, customPlotPCAlgo, plotPCalg, pcalgMB, pcalgNBR, convertPvalueToColorIndex, mapEnrichmentToColors, mapEnrichmentToColorsDual, estimateNetworkDistribution, prob.distr.unif, prob.distr.norm, random.bn.fit, biased.graph, biased.bn.fit, independent.contributions.formula, formulaFalseNeg, independent.contributions.formula.mul, ncpcResampling, logseq, recalculateSVMparams ExportMethods: plot, variableNames, datasetName, dataType, rawData, toDDDataSet, classLabels, signalMatrix, names, ciTest ExportClasses: NCPCRobustness, DDGraphEdge, CITestResult, DDGraph, DDDataSet, FurlongDataSet Package: DECIPHER Exports: Add2DB, Seqs2DB, SearchDB, DB2Seqs, FormGroups, IdentifyByRank, IdLengths, TerminalChar, DistanceMatrix, IdClusters, MODELS, ConsensusSequence, IdConsensus, TileSeqs, FindChimeras, CreateChimeras, DesignArray, Array2Matrix, NNLS, CalculateEfficiencyArray, Amplify, CalculateEfficiencyPCR, DesignPrimers, MeltDNA, CalculateEfficiencyFISH, DesignProbes, BrowseSequences, BrowseDB, AlignSeqs, AlignProfiles, AlignTranslation, MaskAlignment, AlignDB Package: DEDS Exports: aggregateFun, comp.adjp, comp.B, comp.ebayes, comp.F, comp.FC, comp.fdr, comp.modF, comp.modt, comp.SAM, comp.stat, comp.t, comp.unadjp, deds.calcAdjP, deds.calcFDR, deds.checkB, deds.checkclasslabel, deds.checkothers, deds.checkX, deds.chooseTest, deds.genExtra, deds.next.sample, deds.pval, deds.stat, deds.stat.linkC, euclidean, hist.DEDS, pairs.DEDS, qqnorm.DEDS, sam.fdr, sam.multiclass.func, sam.oneclass.func, sam.s0, sam.twoclass.func, test.checkX, topgenes, type2test Package: deepSNV Exports: bam2R, bbb, bf2Vcf, loadAllData, makePrior, manhattanPlot, mcChunk, p.combine, RF ExportMethods: test, summary, show, repeatMask, p.val, normalize, estimateDispersion, estimateDirichlet, deepSNV, coordinates, control, consensusSequence, [ ExportClasses: deepSNV Package: DEGraph Exports: AN.test, BS.test, getConnectedComponentList, getKEGGPathways, getSignedGraph, graph.T2.test, hyper.test, laplacianFromA, plotValuedGraph, randomWAMGraph, testOneConnectedComponent, testOneGraph, twoSampleFromGraph, writeAdjacencyMatrix2KGML Package: DEGreport Exports: createReport, degMV, degMB, degVB, degRank, degPR, degMean, degVar, degPR, degObj Package: DEGseq Exports: DEGexp, DEGexp2, DEGseq, DEGseq, getGeneExp, readGeneExp, samWrapper Package: deltaGseg Exports: parseTraj ExportMethods: chooseBreaks, splitTraj, transformSeries, plotDiff, clusterPV, denoiseSegments, clusterSegments, diagnosticPlots, getAVD, getBreaks, getTNames, getSegments, getTraj, getIntervals, plot, show ExportClasses: SegSeriesTrajectories, SegTrajectories, Trajectories, TransTrajectories Package: derfinder Exports: advancedArg, advanced_arg, analyzeChr, analyze_chr, annotateRegions, annotate_regions, calculatePvalues, calculateStats, calculate_pvalues, calculate_stats, coerceGR, coerce_gr, collapseFullCoverage, collapse_full_coverage, coverageToExon, coverage_to_exon, createBw, createBwSample, create_bw, create_bw_sample, extendedMapSeqlevels, extended_map_seqlevels, filterData, filter_data, findRegions, find_regions, fullCoverage, full_coverage, getRegionCoverage, get_region_coverage, loadCoverage, load_coverage, makeGenomicState, makeModels, make_genomic_state, make_models, mergeResults, merge_results, preprocessCoverage, preprocess_coverage, rawFiles, raw_files, regionMatrix, region_matrix, sampleDepth, sample_depth Package: derfinderHelper Exports: fstats.apply Package: derfinderPlot Exports: plotCluster, plotOverview, plotRegionCoverage, plot_cluster, plot_overview, plot_region_coverage Package: DESeq Exports: newCountDataSet, estimateVarianceFunctions, varianceFitDiagnostics, residualsEcdfPlot, nbinomTest, getBaseMeansAndVariances, nbinomTestForMatrices, estimateSizeFactorsForMatrix, scvPlot, getVarianceStabilizedData, varianceStabilizingTransformation, makeExampleCountDataSet, adjustScvForBias, fitNbinomGLMsForMatrix, fitNbinomGLMs, nbkd.sf, nbinomGLMTest, dispTable, fitInfo, plotDispEsts, plotMA, plotPCA, newCountDataSetFromHTSeqCount ExportMethods: counts, counts<-, sizeFactors, sizeFactors<-, conditions, conditions<-, dispTable, estimateSizeFactors, estimateDispersions ExportClasses: CountDataSet Package: DESeq2 Exports: dispersionFunction<-, dispersions<-, normalizationFactors<-, DESeq, DESeqDataSet, DESeqDataSetFromHTSeqCount, DESeqDataSetFromMatrix, DESeqResults, collapseReplicates, dispersionFunction, dispersions, estimateBetaPriorVar, estimateDispersionsFit, estimateDispersionsGeneEst, estimateDispersionsMAP, estimateDispersionsPriorVar, estimateMLEForBetaPriorVar, estimateSizeFactorsForMatrix, fpkm, fpm, getVarianceStabilizedData, makeExampleDESeqDataSet, nbinomLRT, nbinomWaldTest, normalizationFactors, plotCounts, plotPCA, removeResults, replaceOutliers, replaceOutliersWithTrimmedMean, results, resultsNames, rlog, rlogTransformation, summary.DESeqResults, varianceStabilizingTransformation ExportMethods: sizeFactors, show, plotMA, plotDispEsts, normalizationFactors, estimateSizeFactors, estimateDispersions, dispersions, dispersionFunction, design, counts, sizeFactors<-, design<-, counts<- ExportClasses: DESeqResults, DESeqDataSet Package: DEXSeq Exports: geneIDs, geneIDs<-, groupIDs, groupIDs<-, exonIDs, exonIDs<-, featureIDs, featureIDs<-, DEXSeqHTML, plotDEXSeq, testForDEU, featureCounts, perGeneQValue, DEXSeqDataSet, DEXSeqDataSetFromSE, DEXSeqDataSetFromHTSeq, DEXSeqResults, estimateExonFoldChanges, DEXSeq, sampleAnnotation, newExonCountSet, subsetByGenes, geneCountTable, countTableForGene, modelFrameForGene, estimateExonDispersionsForModelFrame_BM, fitDispersionFunction, read.HTSeqCounts, DEUresultTable, estimatelog2FoldChanges, doCompleteDEUAnalysis, makeCompleteDEUAnalysis_BM, constructModelFrame, estimateDispersions_BM, testGeneForDEU_BM, testForDEU_BM, buildExonCountSet, countReadsForDEXSeq, prepareAnnotationForDEXSeq ExportMethods: estimateDispersions, plotMA, counts, estimateSizeFactors, subsetByOverlaps, findOverlaps, plotDispEsts ExportClasses: ExonCountSet, DEXSeqDataSet, DEXSeqResults Package: dexus Exports: conditionSizes, dexss, dexus, dexus.parallel, dispersions, getSizeNB, INICalls, INIThreshold<-, INIThreshold, INIValues, inputData, logFC, means, normalizeData, normalizedData, params, posteriorProbs, pvals, responsibilities, sampleNames, sizeFactors, sizeParameters, transcriptNames ExportMethods: sort, show, plot, INI, as.data.frame, [ ExportClasses: DEXUSResult Package: DFP Exports: discriminantFuzzyPattern, readCSV, plotMembershipFunctions, showDiscreteValues, showFuzzyPatterns, plotDiscriminantFuzzyPattern, calculateMembershipFunctions, discretizeExpressionValues, calculateFuzzyPatterns, calculateDiscriminantFuzzyPattern ExportMethods: show ExportClasses: ExpressionLevel, LowExpressionLevel, MediumExpressionLevel, HighExpressionLevel Package: DiffBind Exports: dba, dba.peakset, dba.overlap, dba.count, dba.contrast, dba.analyze, dba.report, dba.plotHeatmap, dba.plotPCA, dba.plotMA, dba.plotVenn, dba.plotBox, dba.show, dba.mask, dba.save, dba.load, print.DBA, summary.DBA, plot.DBA, DBA_GROUP, DBA_ID, DBA_TISSUE, DBA_FACTOR, DBA_CONDITION, DBA_TREATMENT, DBA_CONSENSUS, DBA_CALLER, DBA_CONTROL, DBA_REPLICATE, DBA_INTERVALS, DBA_FRIP, DBA_ALL_ATTRIBUTES, DBA_OLAP_PEAKS, DBA_OLAP_ALL, DBA_OLAP_RATE, DBA_COR, DBA_OLAP, DBA_INALL, DBA_SCORE_RPKM, DBA_SCORE_RPKM_FOLD, DBA_SCORE_READS, DBA_SCORE_READS_FOLD, DBA_SCORE_READS_MINUS, DBA_SCORE_TMM_MINUS_FULL, DBA_SCORE_TMM_MINUS_EFFECTIVE, DBA_SCORE_TMM_READS_FULL, DBA_SCORE_TMM_READS_EFFECTIVE, DBA_SCORE_TMM_MINUS_FULL_CPM, DBA_SCORE_TMM_MINUS_EFFECTIVE_CPM, DBA_SCORE_TMM_READS_FULL_CPM, DBA_SCORE_TMM_READS_EFFECTIVE_CPM, DBA_SCORE_SUMMIT, DBA_SCORE_SUMMIT_ADJ, DBA_SCORE_SUMMIT_POS, DBA_READS_DEFAULT, DBA_READS_BAM, DBA_READS_BED, DBA_EDGER, DBA_EDGER_BLOCK, DBA_EDGER_GLM, DBA_EDGER_CLASSIC, DBA_DESEQ, DBA_DESEQ_BLOCK, DBA_DESEQ_GLM, DBA_DESEQ_CLASSIC, DBA_DESEQ2, DBA_DESEQ2_BLOCK, DBA_ALL_METHODS, DBA_ALL_BLOCK, DBA_ALL_METHODS_BLOCK, DBA_DATA_FRAME, DBA_DATA_RANGEDDATA, DBA_DATA_GRANGES, DBA_DATA_SUMMARIZED_EXPERIMENT, DBA_DATA_DBAOBJECT ExportClasses: DBA Package: diffGeneAnalysis Exports: assocAnalysis, biasAdjust, curveFit, dataTrim, normalize, refGroup Package: DirichletMultinomial Exports: dmn, dmngroup, goodnessOfFit, laplace, mixturewt, mixture, heatmapdmn, cvdmngroup, roc, csubset, fitted, predict ExportMethods: AIC, BIC, summary, show ExportClasses: DMN, DMNGroup Package: dks Exports: cred.set, dks, dks.pvalue, pprob.dist, pprob.uniform Package: DMRcate ExportMethods: annotate, rmSNPandCH, dmrcate, makeBedgraphs, DMR.plot, extractRanges Package: DMRforPairs Exports: DMRforPairs, merge_classes, regionfinder, testregion, calc_stats, export_data, plot_annotate_region, plot_annotate_gene, plot_annotate_custom_region, plot_annotate_probes, tune_parameters Package: DNAcopy Exports: CNA, exon.segment, getbdry, segment, segments.p, segments.summary, smooth.CNA, glFrequency, plotSample, zoomIntoRegion Package: DNaseR Exports: footprints Package: domainsignatures Exports: dataSource, getKEGGdata, gseDomain, getKEGGdescription ExportMethods: show ExportClasses: ipDataSource Package: DOQTL Exports: add.missing.F1s, add.slash, addLog, addLogVector, assoc.map, assoc.map.perms, assoc.plot, batch.normalize, bayesint, create.Rdata.files, calc.genoprob, categorize.variants, cc.trans.probs, cluster.strains, coefplot, colSumsLog, condense.model.probs, convert.allele.calls, convert.genotypes, convert.genes.to.GRanges, convert.pos.to.GRanges, convert.variants.to.GRanges, convert.variants.to.numeric, create.genotype.states, create.html.page, create.Rdata.files, do2sanger, do.trans.probs, estimate.cluster.params, extract.raw.data, fast.qtlrel, fill.in.snps, filter.geno.probs, filter.samples, find.overlapping.genes, founder.F1.intensity.plot, gene.plot, get.chr.lengths, get.do.states, get.machine.precision, get.max.geno, get.mgi.features, get.pattern.variants, get.strains, get.variants, get.vcf.strains, genotype.by.sample.barplot, genotype.by.snp.barplot, html.report, intensity.mean.covar.plot, kinship.probs, normalize.batches, permutations.qtl.LRS, prsmth.plot, pxg.plot, qtl.LRS, qtl.qtlrel, qtl.heatmap, qtl.simulate, quantilenorm, rankZ, read.vcf, scanone, scanone.eqtl, scanone.perm, sdp.plot, sex.predict, snp.plot, summarize.genotype.transitions, summarize.by.samples, summarize.by.snps, variant.plot, write.founder.genomes, write.genoprob.plots Package: DOSE Exports: ALLEXTID, EXTID2NAME, EXTID2TERMID, TERM2NAME, TERMID2EXTID, cnetplot, doSim, enrich.internal, enrichDO, enrichMap, geneSim, getALLEG, getGeneSet, gseAnalyzer, gsea, gseaplot, netplot, scaleNodeColor, setReadable, setting.graph.attributes, simplot, theme_dose ExportMethods: summary, show, plot, cnetplot ExportClasses: gseaResult, enrichResult Package: DriverNet ExportMethods: actualEvents, drivers, totalEvents ExportClasses: DriverNetResult Package: DrugVsDisease Exports: generateprofiles, selectrankedlists, classifyprofile, combineProfiles Package: DSS Exports: newSeqCountSet, estDispersion, estNormFactors, waldTest, callDML, callDMR, makeBSseqData ExportMethods: normalizationFactor, normalizationFactor<-, dispersion, dispersion<- ExportClasses: SeqCountSet Package: DTA Exports: tls, DTA.phenomat, DTA.plot.it, DTA.normalize, DTA.map.it, DTA.generate, DTA.estimate, DTA.dynamic.generate, DTA.dynamic.estimate Package: dualKS Exports: dksTrain, dksWeights, dksSelectGenes, dksClassify, dksPerm, KS, dksCustomClass ExportMethods: plot, show, summary ExportClasses: DKSGeneScores, DKSClassifier, DKSPredicted Package: DupChecker Exports: arrayExpressDownload, buildFileTable, geoDownload, validateFile Package: DynDoc Exports: baseVigDesc, editVignetteCode, getPkgVigList, getVigInfo, getVigInfoNames, getVignette, getVignetteCode, getVignetteHeader, hasVigHeaderField, tangleToR, tangleToRFinish, tangleToRRuncode, tangleToRSetup, .transformNames, transformVigInfoLine ExportMethods: chunk<-, chunk, chunkList, chunkName, chunks, codeChunk, codeChunks, evalChunk, evalEnv, getAllCodeChunks, getChunk, getDepends, getKeywords, getOptions, getRequires, getSuggests, indexEntry, numChunks, numOptions, path, pdfPath, setChunk<-, show, summary, SweaveOptions, vigPackage, vigPkgVersion ExportClasses: chunkList, codeChunk, DynDoc, SweaveOptions, Vignette, vignetteCode Package: EasyqpcR Exports: nrmData, calData, totData, badCt, slope Package: easyRNASeq Exports: BamFileList, IRanges, RangedData, SRFilterResult, chastityFilter, chromosomeFilter, compose, nFilter, naPositionFilter, readAligned ExportMethods: yieldSize, writeFastq, width, validate, unsafeAppend, type, transcriptCounts, stranded, strand, srFilter, split, simpleRNASeq, seqnames, reduce, readLength, readCoverage, readCounts, ranges, precision, plotNormalizationFactors, plotDispersionEstimates, plotDispLSD, parallelize, paired, organismName, multivariateConditions, librarySize, knownOrganisms, getBamFileList, getAnnotation, genomicAnnotation, geneModel, geneCounts, fileName, fetchCoverage, fetchAnnotation, featureCounts, exonCounts, easyRNASeq, demultiplex, datasource, countBy, count, colnames, chrSize, barcodePlot, bamParam, assay, annotParam, SummarizedExperiment, RnaSeqParam, RPKM, BamParam, AnnotParam, strand<-, readLength<-, readCoverage<-, readCounts<-, organismName<-, librarySize<-, genomicAnnotation<-, geneModel<-, fileName<-, chrSize<- ExportClasses: SummarizedExperiment, RnaSeqParam, RangedData, RNAseq, BamParam, BamFileList, AnnotParamObject, AnnotParamCharacter, AnnotParam Package: EBarrays Exports: checkCCV, checkModel, checkVarsMar, checkVarsQQ, crit.fun, eb.createFamilyGG, eb.createFamilyLNN, eb.createFamilyLNNMV, ebPatterns, emfit, emfit0, emfit1, emfit2, emfit3, emfitmv, plot.ebarraysEMfit, plotCluster, plotMarginal, postprob Package: EBcoexpress Exports: bwmc, crit.fun, makeMyD, initializeHP, priorDiagnostic, showPair, showNetwork, ebCoexpressFullTCAECM, ebCoexpressOneStep, ebCoexpressZeroStep, ebCoexpressMeta, rankMyGenes Package: EBImage Exports: Image, is.Image, as.Image, Grayscale, Color, colorMode, colorMode<-, imageData, imageData<-, getFrame, numberOfFrames, readImage, writeImage, display, resize, rotate, flip, flop, translate, affine, transpose, thresh, bwlabel, otsu, watershed, propagate, ocontour, paintObjects, rmObjects, reenumerate, colorLabels, filter2, gblur, medianFilter, equalize, makeBrush, erode, dilate, opening, closing, erodeGreyScale, dilateGreyScale, openingGreyScale, closingGreyScale, whiteTopHatGreyScale, blackTopHatGreyScale, selfcomplementaryTopHatGreyScale, distmap, floodFill, fillHull, rgbImage, channel, toRGB, stackObjects, tile, untile, drawCircle, computeFeatures, computeFeatures.basic, computeFeatures.shape, computeFeatures.moment, computeFeatures.haralick, standardExpandRef, localCurvature, getNumberOfFrames, blur, drawtext, drawfont, getFeatures, hullFeatures, zernikeMoments, edgeProfile, edgeFeatures, haralickFeatures, haralickMatrix, moments, cmoments, smoments, rmoments ExportMethods: Math2, normalize, combine, hist, show, Ops, [ ExportClasses: Image Package: EBSeq Exports: crit_fun, DenNHist, EBTest, GetNg, GetPP, MedianNorm, PolyFitPlot, PostFC, QQP, QuantileNorm, RankNorm, EBMultiTest, GetMultiPP, GetPatterns, PlotPattern, GetPPMat, GetMultiFC, PlotPostVsRawFC, GetNormalizedMat, f0, f1, LogN, LogNMulti Package: EBSeqHMM Exports: EBTest_ext, EBHMMNBfunForMulti, EBHMMNBMultiEM_2chain, EBHMMNBfun, beta.mom, LikefunNBHMM, f0, GetDECalls, GetConfidentCalls, EBSeqHMMTest, GetAllPaths, PlotExp Package: ecolitk Exports: arrowsArc, chromPos2angle, cPlotCircle, ecoli.len, gccontent, linesArc, linesChrom, linesCircle, linkedmultiget, pointsArc, polar2xy, polygonArc, polygonChrom, polygonDisk, rotate, wstringapply, xy2polar Package: EDASeq Exports: newSeqExpressionSet, plotQuality ExportMethods: length, width, initialize, barplot, plot, plotQuality, exprs, offst, offst<-, boxplot, meanVarPlot, biasPlot, plotNtFrequency, withinLaneNormalization, betweenLaneNormalization, biasBoxplot, MDPlot, plotRLE, plotPCA, normCounts, normCounts<-, counts, counts<- ExportClasses: SeqExpressionSet Package: EDDA Exports: generateData, testDATs, computeAUC, plotROC, plotPRC Package: edgeR ExportMethods: show ExportClasses: DGEList, DGEExact, DGEGLM, DGELRT, TopTags Package: eiR Exports: eiInit, eiMakeDb, eiQuery, eiAdd, eiPerformanceTest, eiCluster, setDefaultDistance, addTransform, loadLSHData, freeLSHData Package: eisa Exports: ISA, ISANormalize, ISAIterate, ISAUnique, ISASweep, ISASweepGraph, ISASweepGraphPlot, ISARobustness, ISAFilterRobust, ISAEnrichment, ISAGO, ISAKEGG, ISACHR, ISAmiRNA, gograph, gographPlot, expPlotCreate, expPlotColbar, expPlot, condPlot, overlap, overlapPlot, mnplot, ISAmnplot, ISA2heatmap, profilePlot, ISAHTMLTable, ISAHTMLModules, ISAHTML, annotate ExportMethods: coerce, summary, htmlReport, pvalues, geneCounts, oddsRatios, expectedCounts, universeCounts, universeMappedCount, geneMappedCount, geneIdUniverse, geneIdsByCategory, sigCategories, makeValidParams, ontology, ontology<-, conditional, conditional<-, drive, drive<-, hyperGTest, seedData, runData, getFeatures, getSamples, getFeatureNames, getSampleNames, getFeatureMatrix, getSampleMatrix, getFullFeatureMatrix, getFullSampleMatrix, getFeatureScores, getSampleScores, getNoFeatures, getNoSamples, featureThreshold, sampleThreshold, getOrganism, featExprs, sampExprs, prenormalized, prenormalized<-, hasNA, hasNA<- Package: ELBOW Exports: analyze_elbow, do_elbow_rnaseq, do_elbow, elbow_variance, extract_working_sets, get_elbow_limma, get_pvalue, null_variance, plot_dataset, plot_elbow, replicates_to_fold Package: EnrichmentBrowser Exports: read.eset, de.ana, pdistr, volcano, exprs.heatmap, probe.2.gene.eset, get.kegg.genesets, parse.genesets.from.GMT, sbea.methods, sbea, gs.ranking, download.kegg.pathways, compile.grn.from.kegg, nbea.methods, nbea, ggea.graph, ggea.graph.legend, ea.browse, comb.ea.results, ebrowser Package: ENVISIONQuery Exports: getServices, getServiceNames, getService, getServiceOptions, getToolNames, getTool, getServiceClient, getInputTypes, ENVISIONQuery Package: epigenomix Exports: chipVals, chipVals<-, cpm, ChIPseqSet, chains, classification, components, convergence, mmData, listClassificationMethods, weights, bayesMixModel, calculateCrossCorrelation, getAlignmentQuality, integrateData, matchProbeToPromoter, mlMixModel, normalizeChIP, plotChains, plotClassification, plotComponents, summarizeReads ExportMethods: dim, length, show, summary ExportClasses: ChIPseqSet, MixModel, MixModelBayes, MixModelML, MixtureComponent Package: epivizr Exports: startEpiviz, startStandalone, makeGeneTrackAnnotation ExportClasses: EpivizDeviceMgr, EpivizData, EpivizTrackData, EpivizFeatureData, EpivizBlockData, EpivizBpData, EpivizGeneInfoData, EpivizChart Package: erccdashboard Exports: annotLODR, dynRangePlot, erccROC, estLODR, est_r_m, geneExprTest, initDat, maSignal, multiplot, runDashboard, saveERCCPlots Package: ExiMiR Exports: ReadExi, createAB, NormiR, bg.correct.miR, norm.miR, summarize.miR, NormiR.bgcorrect.methods, NormiR.normalize.methods, NormiR.pmcorrect.methods, NormiR.summary.methods, NormiR.spikein.args, make.gal.env Package: exomeCopy Exports: subdivideGRanges, countBamInGRanges, getGCcontent, generateBackground, exomeCopy, copyCountSegments, plot.ExomeCopy, compileCopyCountSegments, plotCompiledCNV, negLogLike, viterbiPath ExportMethods: show, plot ExportClasses: ExomeCopy Package: exomePeak Exports: ctest, rhtest, exomepeak, bltest Package: ExpressionView Exports: LaunchEV ExportMethods: ExportEV, OrderEV Package: fabia Exports: fabia, fabias, fabiap, spfabia, readSamplesSpfabia, samplesPerFeature, readSpfabiaResult, mfsc, fabiasp, fabi, projFunc, projFuncPos, estimateMode, nmfsc, nmfeu, nmfdiv, matrixImagePlot, plotBicluster, extractPlot, extractBic, makeFabiaData, makeFabiaDataBlocks, makeFabiaDataPos, makeFabiaDataBlocksPos, fabiaDemo, fabiaVersion ExportMethods: plot, summary, show, showSelected, parameters, n, p1, p2, l, center, scaleData, X, L, Z, M, LZ, U, avini, xavini, ini, Psi, lapla, parameters<-, n<-, p1<-, p2<-, l<-, center<-, scaleData<-, X<-, L<-, Z<-, M<-, LZ<-, U<-, avini<-, xavini<-, ini<-, Psi<-, lapla<- ExportClasses: Factorization Package: factDesign Exports: contrastTest, findFC, kRepsOverA, madOutPair, outlierPair, par2lambda Package: farms Exports: expFarms, qFarms, lFarms, generateExprVal.method.farms ExportMethods: summary, plot, INIcalls, getI_Eset, getNI_Eset, getI_ProbeSets, getNI_ProbeSets ExportClasses: INI_Calls Package: fastLiquidAssociation Exports: fastMLA, mass.CNM, fastboots.GLA ExportMethods: fastMLA, mass.CNM, fastboots.GLA ExportClasses: fastMLA, mass.CNM, fastboots.GLA Package: fastseg Exports: fastseg, segPlot, toDNAcopyObj Package: fdrame Exports: compute.f.statistic, compute.resampling.stat, compute.statistic, compute.t.statistic, fdr.adaptive.c, fdr.adaptive.c.resampling, fdr.basic.comp, fdr.bh, fdr.error, fdr.gui, fdr.ma, fdr.plot, fdr.pt, fdr.q, fdr.qu, gene.expression.normalization, get.resampling.statistic.array, OnBrowseDesign, OnBrowseInput, OnBrowseOutput, OnCancel, OnCbfa1, OnCbfa2, OnCbfa3, OnCbfa4, OnCompute, OnHelp, OnOK, OnRbfa1, OnRbfa2, OnRbfa3, OnRbfa4, OnRbpm1, OnRbpm2, read.matrix Package: ffpe Exports: CATplot ExportMethods: sampleQC, sortedIqrPlot Package: FGNet Exports: FGNet_GUI, FGNet_report, fea_gtLinker, fea_gtLinker_getResults, fea_david, fea_gage, fea_topGO, format_david, format_results, readGeneTermSets, fea2incidMat, functionalNetwork, clustersDistance, analyzeNetwork, getTerms, plotGoAncestors, keywordsTerm, plotKegg Package: flagme ExportMethods: show, plot ExportClasses: peaksDataset Package: flipflop Exports: flipflop Package: flowBeads Exports: BeadFlowFrame, mefTransform ExportMethods: toMEF, relativeNormalise, plot, length, hasMEF, getTransformFunction, getParams, getMEFtransform, getMEFparams, getDate, getClusteringStats, generateReport, gateBeads, absoluteNormalise ExportClasses: GatedBeadFlowFrame, BeadFlowFrame Package: flowBin Exports: checkQNorm, flowBin ExportMethods: tube.set, tube.set<-, show, removeSparseBins, quantileNormalise, name, name<-, measure.pars, measure.pars<-, mapBinsKNN, kMeansBin, getBinExpr, flowFPBin, eventsInBins, control.tubes, control.tubes<-, checkQNorm, bin.pars, bin.pars<-, bin.labels, bin.labels<- ExportClasses: FlowSample, BinnedFlowSample Package: flowcatchR Exports: Frames, add.contours, channel.Frames, crop.Frames, export.Frames, export.particles, inspect.Frames, kinematics, link.particles, matchTrajToParticles, normalizeFrames, particles, penaltyFunctionGenerator, plot2D.TrajectorySet, preprocess.Frames, read.Frames, read.particles, rotate.Frames, select.Frames, select.particles, shinyFlow, snap, trajectories ExportMethods: show ExportClasses: TrajectorySet, ParticleSet, LinkedParticleSet, KinematicsFeaturesSet, KinematicsFeatures, Frames Package: flowCHIC Exports: fcs_to_img, img_sub, calculate_overlaps_xor, plot_nmds ExportMethods: fcs_to_img, img_sub, calculate_overlaps_xor, plot_nmds Package: flowCL Exports: flowCL, test.flowCL.connection Package: flowClean Exports: clean Package: flowClust Exports: flowClust2Prior ExportMethods: show, summary, plot, density, hist, filter, %in%, [, [[, length, coerce, coerce<-, Subset, split, ruleOutliers, ruleOutliers<-, Map, criterion, criterion<-, mkPrior ExportClasses: flowClust, flowClustList, tmixFilter, tmixFilterResult, tmixFilterResultList Package: flowCore Exports: action, actions, add, alias, arcsinhTransform, asinht, asinhtGml2, as.data.frame.manyFilterResult, assign, biexponentialTransform, boundaryFilter, char2ExpressionFilter, cleanup, colnames<-, compensate, compensatedParameter, compensateView, compensateActionItem, compensation, Data, dg1polynomial, each_col, each_row, EHtrans, ellipsoidGate, exponential, expressionFilter, fcActionReference, fcAliasReference, fcCompensateReference, fcDataReference, fcFilterReference, fcFilterResultReference, fcNormalizationReference, fcReference, fcSubsettingReference, fcTransformReference, fcTreeReference, fcViewReference, filter, filterDetails, filterDetails<-, filterList, filters, filtersList, filterReference, filterSet, flowFrame, flowSet, fsApply, gate, gateActionItem, gateView, head, hyperlog, hyperlogtGml2, identifier, identifier<-, invsplitscale, isFCSfile, isNull, journal, kmeansFilter, keyword, keyword<-, linearTransform, lintGml2, lnTransform, logarithm, logtGml2, logTransform, logicletGml2, logicleTransform, FCSTransTransform, inverseLogicleTransform, ls, manyFilterResult, norm2Filter, nodes, normalization, normalizeActionItem, normalizeView, fcNullReference, parameters, parameters<-, parent, polygonGate, polytopeGate, print, quadGate, quadratic, quadraticTransform, ratio, ratiotGml2, read.FCS, read.FCSheader, read.flowSet, rectangleGate, Rm, sampleFilter, scaleTransform, sinht, sort, spillover, split, splitscale, splitScaleTransform, squareroot, Subset, subsettingActionItem, subsetting, summarizeFilter, tail, timeFilter, toTable, truncateTransform, transformActionItem, transformList, transformReference, transformView, tree, undo, unitytransform, view, views, workFlow, write.FCS, write.flowSet, %&%, %in%, %subset%, %on%, estimateLogicle, getChannelMarker ExportMethods: action, actions, add, alias, assign, c, cbind2, coerce, colnames, colnames<-, compensate, Data, description, description<-, dim, each_row, each_col, eval, exprs, exprs<-, featureNames, filter, filterDetails, filterDetails<-, filterReference, fsApply, gate, get, getIndexSort, head, identifier, identifier<-, initialize, isNull, journal, keyword, keyword<-, length, ls, mget, names, ncol, nodes, normalize, nrow, parameters, parameters<-, parent, pData, pData<-, phenoData, phenoData<-, plot, print, range, rbind2, Rm, sampleNames, sampleNames<-, show, sort, spillover, split, Subset, summarizeFilter, summary, tail, toTable, transform, tree, varLabels, varLabels<-, varMetadata, varMetadata<-, %in%, %on%, %subset%, <, <=, ==, >, >=, |, !, [, [[, [[<-, $, *, &, %&% ExportClasses: actionItem, asinht, asinhtGml2, boundaryFilter, compensation, compensateActionItem, compensatedParameter, compensateView, complementFilter, concreteFilter, dg1polynomial, EHtrans, ellipsoidGate, exponential, expressionFilter, fcActionReference, fcAliasReference, fcCompensateReference, fcDataReference, fcFilterReference, fcFilterResultReference, fcNormalizationReference, fcNullReference, fcReference, fcStructureReference, fcSubsettingReference, fcTransformReference, fcTreeReference, fcViewReference, filter, filterList, filters, filtersList, filterReference, filterResult, filterResultList, filterSet, filterSummary, filterSummaryList, flowFrame, flowSet, gateActionItem, gateView, hyperlog, hyperlogtGml2, intersectFilter, invsplitscale, kmeansFilter, lintGml2, logarithm, logicalFilterResult, logicletGml2, logtGml2, manyFilterResult, multipleFilterResult, normalization, normalizeActionItem, normalizeView, norm2Filter, parameters, parameterTransform, parameterFilter, polygonGate, polytopeGate, quadGate, quadratic, randomFilterResult, ratio, ratiotGml2, rectangleGate, sampleFilter, setOperationFilter, sinht, splitscale, squareroot, subsetFilter, subsettingActionItem, subsetting, timeFilter, transform, transformActionItem, transformFilter, transformMap, transformList, transformReference, transformView, unionFilter, unitytransform, view, workFlow Package: flowCyBar Exports: normalize, cybar_plot, nmds, correlation ExportMethods: normalize, cybar_plot, nmds, correlation Package: flowDensity Exports: flowDensity, plot, getflowFrame, .flowDensity, deGate, plotDens, notSubFrame, nmRemove ExportClasses: CellPopulation Package: flowFit Exports: parentFitting, logTicks, proliferationGrid, generationsDistance, proliferationFitting, proliferationIndex, getGenerations ExportMethods: initialize, show, summary, Data, confint, coef, plot ExportClasses: parentFittingData, proliferationFittingData Package: flowFlowJo Exports: readFlowJoList, getFlowJoGates, collectSummaryFlowInfo, getFlowJoSummary, createFlowReport, simplifyGateNames, flowJoCompensate, getWellId ExportClasses: flowJoObj, flowJoList, fcsSummary, fcsSummaryList Package: flowFP Exports: flowFPModel, is.flowFPModel, flowFP, is.flowFP, flowFPPlex, is.flowFPPlex ExportMethods: show, summary, name, tags, sampleNames, sampleClasses, sampleClasses<-, hasClasses, counts, nFeatures, nInstances, binBoundary, nRecursions, nRecursions<-, length, length<-, parameters, plot, append, [, [[ ExportClasses: flowFPModel, flowFP, flowFPPlex Package: flowMap Exports: FRmapping, FRmappingSimple, getFR, getFRest, getFRmat, getFRvalsPerm, getMatched, makeCrossMap, makeRefMap, makeRefSample, makeSampleInfo, permutePops, statCrossLists, getSomePops ExportMethods: getWnulls, getSampleInfo, getRefData, getPopFilt, getPnulls, getPnorm, getPairList, getNewPops, getMatchPairs, getMatchMat, getFRstats, getFRmapStats, getFRmapPnulls, getFRmapPnorms, getCrossList ExportClasses: somePops, refSample, refMap, matchMat, crossMap, SampleInfo, FRvalsPerm, FRstats Package: flowMatch Exports: Cluster, ClusteredSample, mahalanobis.dist, symmetric.KL, dist.cluster, dist.matrix, dist.sample, dist.template, match.clusters, match.clusters.dist, create.template, template.tree, MetaCluster, Template ExportMethods: plot, summary, get.size, get.dimension, get.center, get.cov, get.cluster.id, get.sample.id, get.num.clusters, get.clusters, get.labels, get.num.metaclusters, get.template.id, get.metaClusters, get.tree, get.match12, get.match21, get.matching.cost, get.unmatch.penalty, sample.id<- ExportClasses: Cluster, ClusteredSample, ClusterMatch, MetaCluster, Template Package: flowMeans Exports: flowMeans, changepointDetection, plot, summary, show Package: flowMerge Exports: fitPiecewiseLinreg, pFlowMerge, checkForRemoteErrors, flowObj, ENT, NENT, BIC, ICL, split, map, ptree ExportMethods: getData, merge, plot, summary, show, split ExportClasses: flowMerge, flowObj Package: flowPeaks Exports: flowPeaks, adjust.flowPeaks, assign.flowPeaks, evalCluster Package: flowPlots Exports: GroupListBoxplot, makeDataList, makeBarplotData, makeTernaryData, legendPFDStatsGroupNames, computePFDGroupStatsList ExportMethods: stackedData, pfdData, pfdPartsData, marginalData, markers, profileData, stackedData<-, pfdData<-, pfdPartsData<-, marginalData<-, markers<-, profileData<-, computeMarkers, readStackedData, computeProfileData, computeMarginalData, computePFDData, computePFDPartsData ExportClasses: StackedData Package: flowQ Exports: validProcess, qaProcess, aggregatorList, qaGraph, qaGraphList, qaProcessFrame, writeQAReport, qaReport, qaProcess.marginevents, qaProcess.timeline, qaProcess.timeflow, qaProcess.cellnumber, qaProcess.2DStatsPlot, qaProcess.ECDFPlot, qaProcess.DensityPlot, qaProcess.KLDistPlot, qaProcess.BoundaryPlot, locateDuplicatedParameters, normalizeSets, writeQATextReport, txtFormatQAObject, preProcessFlowList, binaryAggregator, discreteAggregator, factorAggregator, stringAggregator, numericAggregator, rangeAggregator, evaluateProcess ExportMethods: outliers, initialize, show, names, writeLines ExportClasses: outlierResult, qaAggregator, binaryAggregator, discreteAggregator, factorAggregator, stringAggregator, numericAggregator, rangeAggregator, aggregatorList, qaGraph, qaGraphList, qaProcessFrame, qaProcess, qaProcessSummary Package: flowQB Exports: BEADflowQBCalculation, find_peak, scatter_gate, LEDflowQBCalculation Package: flowStats Exports: lymphGate, lymphFilter, curv1Filter, curv2Filter, oneDGate, quadrantGate, rangeGate, rangeFilter, warpSet, proBin, binByRef, gaussNorm, plotBins, calcPearsonChi, calcPBChiSquare, gpaSet, iProcrustes, normQA, singletGate ExportMethods: %in%, normalize ExportClasses: lymphFilter, rangeFilter, curv1Filter, curv2Filter Package: flowTrans Exports: flowTrans, extractParams, summary.flowTransResult ExportMethods: flowTrans Package: flowType Exports: flowType, decodePhenotype, plot, summary, getLabels, encodePhenotype, calcNumPops, calcMemUse ExportClasses: Phenotypes Package: flowUtils Exports: read.gatingML, testGatingMLCompliance, write.gatingML Package: flowViz Exports: addName, flowViz.par.set, flowViz.par.get, glines, gpoints, glpoints, glpolygon, gpolygon, panel.densityplot.flowset, panel.ecdfplot.flowset, panel.xyplot.flowframe, panel.xyplot.flowframe.time, panel.xyplot.flowset, prepanel.ecdfplot.flowset, prepanel.densityplot.flowset, prepanel.xyplot.flowframe, prepanel.xyplot.flowframe.time, prepanel.xyplot.flowset, timeLinePlot ExportMethods: addName, contour, densityplot, ecdfplot, flowPlot, glines, gpoints, gpolygon, glpoints, glpolygon, levelplot, parallel, plot, qqmath, splom, timeLinePlot, xyplot Package: flowWorkspace Exports: flowData<-, GatingSetList, archive, booleanFilter, char2booleanFilter, closeWorkspace, flowData, flowJoTrans, flowWorkspace.par.get, flowWorkspace.par.set, getChildren, getCompensationMatrices, getData, getFJWSubsetIndices, getGate, getIndiceMat, getKeywords, getLoglevel, getNodes, getParent, getPopStats, getProp, getSample, getSampleGroups, getSamples, getSingleCellExpression, getTotal, getTransformations, isNcdf, load_gs, load_gslist, mkformula, openWorkspace, parseWorkspace, plotGate, plotPopCV, prettyAxis, save_gs, save_gslist, setGate, setLoglevel, setNode, summary, unarchive ExportMethods: transform, show, setNode, setGate, sampleNames, recompute, rbind2, plotPopCV, plotGate, plot, parseWorkspace, pData, openWorkspace, length, lapply, keyword, getTotal, getSingleCellExpression, getSamples, getSampleGroups, getProp, getPopStats, getParent, getNodes, getKeywords, getIndices, getGate, getData, getCompensationMatrices, getChildren, flowData, filterObject, closeWorkspace, clone, add, Rm, GatingSet, sampleNames<-, pData<-, flowData<-, [[, [ ExportClasses: flowJoWorkspace, booleanFilter, GatingSetList, GatingSet, GatingHierarchy Package: fmcsR Exports: fmcs, fmcsBatch, plotMCS, mcs2sdfset ExportMethods: stats, mcs1, mcs2, [[, coerce, show ExportClasses: MCS Package: focalCall Exports: focalCall, FreqPlot, FreqPlotfocal, igvFiles, singleSample ExportClasses: cghCall Package: FourCSeq Exports: FourC, addFragments, addPeaks, addViewpointFrags, combineFragEnds, countFragmentOverlaps, countFragmentOverlapsSecondCutter, distFitMonotone, distFitMonotoneSymmetric, findViewpointFragments, getAllResults, getDifferences, getDistAroundVp, getNormalizationFactors, getReferenceSeq, getZScores, normalizeRPM, plotDifferences, plotFits, plotNormalizationFactors, plotScatter, plotZScores, smoothCounts, smoothHitPerCent, writeTrackFiles ExportClasses: FourC Package: frma Exports: frma, barcode, GNUSE ExportMethods: initialize, se.exprs, weights, residuals, randomeffects, se.exprs<-, weights<-, residuals<-, randomeffects<- ExportClasses: frmaExpressionSet Package: frmaTools Exports: makeVectorsAffyBatch, makeVectorsFeatureSet, makeVectorPackage, convertPlatform Package: FunciSNP Exports: getFSNPs, FunciSNPAnnotateSummary, FunciSNPplot, FunciSNPbed, FunciSNPtable, FunciSNPsummaryOverlaps, FunciSNPidsFromSummary, alt.allele<-, alt.allele, chr<-, chr, correlated.snps<-, correlated.snps, yafsnp.dprime<-, yafsnp.dprime, genotype<-, genotype, pop.genotype, pop.genotype<-, overlapping.features<-, overlapping.features, population<-, population, position<-, position, ref.allele<-, ref.allele, yafsnp.rsq<-, yafsnp.rsq, yafsnp.pvalue, yafsnp.pvalue<-, snpid<-, snpid ExportMethods: alt.allele<-, alt.allele, chr<-, chr, correlated.snps<-, correlated.snps, yafsnp.dprime<-, yafsnp.dprime, genotype<-, genotype, pop.genotype, pop.genotype<-, overlapping.features<-, overlapping.features, population<-, population, position<-, position, ref.allele<-, ref.allele, yafsnp.rsq<-, yafsnp.rsq, yafsnp.pvalue, yafsnp.pvalue<-, snpid<-, snpid ExportClasses: CorrelatedSNPs, TagSNP, TSList Package: gaga Exports: adjustfitNN, checkfit, classpred, dcgamma, findgenes, fitGG, fitNN, fitNNSingleHyp, forwsimDiffExpr, geneclus, getpar, mcgamma, parest, posmeansGG, powfindgenes, rcgamma, simGG, simLNN, simNN, simnewsamples, powclasspred, seqBoundariesGrid, buildPatterns, plotForwSim Package: gage Exports: eg2sym, sym2eg, essGene, esset.grp, gage, gagePrep, gageSum, gageComp, gagePipe, geneData, gs.tTest, gs.zTest, gs.KSTest, heter.gage, pairData, go.gsets, kegg.gsets, readExpData, readList, sigGeneSet Package: gaggle Exports: gaggleInit, getNameList, getCluster, getMatrix, getNetwork, getTuple, broadcast, geese, getTargetGoose, setTargetGoose, setSpecies, getSpecies, showGoose, hideGoose, testGagglePackage, connectToGaggle, disconnectFromGaggle, getJavaClassName, getTupleAsList, tupleToList, newSingle, addSingle, newTuple Package: gaia Exports: runGAIA, load_cnv, load_markers Package: gaucho Exports: gaucho, gauchoReport Package: gCMAP Exports: annotate_eset_list, center_eSet, eSetOnDisk, generate_gCMAP_NChannelSet, eset_instances, go2cmap, KEGG2cmap, mapNmerge, memorize, mergeCMAPs, reactome2cmap, signedRankSumTest, splitPerturbations, wiki2cmap, zScores ExportMethods: camera_score, CMAPCollection, cmapTable, connectivity_score, downIds, docs, docs<-, effect, effect<-, errors, errors<-, featureScores, fisher_score, gsealm_score, gsealm_jg_score, geneIds, geneIndex, geneScores, geneSign, geneSign<-, incidence, induceCMAPCollection, initialize, labels, labels<-, mapIdentifiers, mergeCollections, members, mgsa_score, minSetSize, plot, padj, padj<-, pval, pval<-, mroast_score, romer_score, set, set<-, setSizes, show, signed, signed<-, SignedGeneSet, nFound, nFound<-, trend, trend<-, upIds, nSet, nSet<-, wilcox_score, zscores ExportClasses: SignedGeneSet, CMAPCollection, CMAPResults Package: gCMAPWeb Exports: exampleCMAP, examplePost, gCMAPWeb, load_cmaps, validate_config_file Package: gcrma Exports: average.for.PAV, base.profiles, base.profiles.mm, base.profiles.nc, bg.adjust.affinities, bg.adjust.constant, bg.adjust.fullmodel, bg.adjust.gcrma, bg.adjust.mm, bg.adjust.optical, bg.parameters.ns, check.probes, compute.affinities, compute.affinities2, compute.affinities.local, compute.affinity.coef, fast.bkg, gcrma, gcrma.bg.transformation, gcrma.bg.transformation.fast, gcrma.engine, gcrma.engine2, getCDF, getProbePackage, just.gcrma, justGCRMA, left.sigma, mem.bkg, PAV, plotBaseProfiles, GSB.adj Package: gdsfmt Exports: add.gdsn, addfile.gdsn, addfolder.gdsn, append.gdsn, apply.gdsn, assign.gdsn, cache.gdsn, cleanup.gds, closefn.gds, clusterApply.gdsn, cnt.gdsn, compression.gdsn, createfn.gds, delete.attr.gdsn, delete.gdsn, diagnosis.gds, get.attr.gdsn, getfile.gdsn, index.gdsn, is.element.gdsn, lasterr.gds, ls.gdsn, moveto.gdsn, name.gdsn, objdesp.gdsn, openfn.gds, print.gds.class, print.gdsn.class, put.attr.gdsn, read.gdsn, readex.gdsn, readmode.gdsn, rename.gdsn, setdim.gdsn, showfile.gds, sync.gds, system.gds, write.gdsn Package: geecc Exports: runConCub, filterConCub, plotConCub, GO2list, KEGG2list, p.value, p.value<-, minimum.l2or, minimum.l2or<-, test.direction, test.direction<-, skip.zeroobs, skip.zeroobs<-, skip.min.obs, skip.min.obs<-, skip.min.group, skip.min.group<-, drop.insignif.layer, drop.insignif.layer<-, drop.wrongdir.layer, drop.wrongdir.layer<-, drop.lowl2or.layer, drop.lowl2or.layer<- ExportMethods: show, initialize, getTable ExportClasses: concub, concubfilter Package: genArise Exports: a.arise, alter.unique, analysis.window, annotations, back.gui, bg.correct, create.project, cys.plot, filter.spot, genArise, genArise.init, genMerge, get.values, get.Zscore, global.norm, graphic.choose, grid.norm, help, i.arise, imageLimma, m.arise, ma.plot, make.swap, meanUnique, note, old.project, post.analysis, principal, projects.select, r.arise, read.dataset, read.spot, reset.history, ri.plot, set.grid.properties, set.history.project, set.path.project, set.project.properties, single.norm, spotUnique, swap.select, trim, write.dataSet, write.spot, write.zscore, Zscore, Zscore.plot, Zscore.points ExportClasses: Spot, DataSet Package: GENE.E Exports: from.genee, to.genee Package: GeneAnswers Exports: categoryNet, chartPlots, drawTable, geneAnnotationHeatmap, geneAnswersBuilder, geneAnswersChartPlots, geneAnswersConceptNet, geneAnswersConcepts, geneAnswersHeatmap, geneAnswersHomoMapping, geneAnswersReadable, geneAnswersSort, geneConceptNet, getCategoryList, getCategoryTerms, getConceptTable, getDOLiteTerms, getGOList, getHomoGeneIDs, getPATHList, getPATHTerms, getSymbols, groupReport, getListGIF, searchEntrez, topCategory, topCategoryGenes, topDOLITE, topDOLITEGenes, topGO, topGOGenes, topPATH, topPATHGenes, topREACTOME.PATH, topREACTOME.PATHGenes, topcaBIO.PATH, topcaBIO.PATHGenes, geneAnswersConceptRelation, getConnectedGraph, getMultiLayerGraphIDs, getSingleLayerGraphIDs, getNextGOIDs, buildNet, getTotalGeneNumber, getREACTOMEPATHList, getREACTOMEPATHTerms, getcaBIOPATHList, getcaBIOPATHTerms, entrez2caBIO, caBIO2entrez ExportMethods: getGeneInput, getTestType, getPValueT, getGenesInCategory, getGeneExprProfile, getAnnLib, getCategoryType, getEnrichmentInfo, setGeneInput, setTestType, setPValueT, setGeneExprProfile, setAnnLib, setCategoryType, setGenesInCategory, setEnrichmentInfo ExportClasses: GeneAnswers Package: GeneExpressionSignature Exports: getRLs, RankMerging, ScorePGSEA, ScoreGSEA, SignatureDistance Package: genefilter Exports: Anova, allNA, anyNA, coxfilter, cv, eSetFilter, varFilter, featureFilter, fastT, ttest, shorth, half.range.mode, rowttests, colttests, rowFtests, colFtests, rowSds, rowVars, dist2, filterfun, findLargest, gapFilter, genefilter, genescale, getFilterNames, getFuncDesc, getRdAsText, isESet, kOverA, maxA, pOverA, parseArgs, parseDesc, setESetArgs, showESet, kappa_t, kappa_p, filtered_p, filtered_R, rejection_plot, filter_volcano ExportMethods: genefinder, show, plot, [, sens, spec, area, pAUC, AUC, rowpAUCs, nsFilter ExportClasses: rowROC Package: GeneGA Exports: GeneGA, GeneFoldGA, GeneCodon ExportMethods: show, plotGeneGA ExportClasses: GeneGA, GeneFoldGA Package: GeneMeta Exports: CountPlot, dstar, f.Q, IDRplot, multExpFDR, mu.tau2, sigmad, tau2.DL, var.tau2, zScoreFDR, zScorePermuted, zScores ExportMethods: getdF Package: GeneNetworkBuilder Exports: convertID, buildNetwork, filterNetwork, polishNetwork, uniqueExprsData Package: GeneOverlap Exports: newGeneOverlap, newGOM ExportMethods: show, print, getListA, setListA<-, getListB, setListB<-, getIntersection, getUnion, getGenomeSize, setGenomeSize<-, getTested, getContbl, getPval, getOddsRatio, getJaccard, testGeneOverlap, getGsetA, getGsetB, getSelfCompare, getMatrix, getNestedList, [, drawHeatmap ExportClasses: GeneOverlap, GeneOverlapMatrix Package: geneplotter Exports: alongChrom, cColor, cPlot, cScale, dChip.colors, greenred.colors, GetColor, plotChr, plotExpressionGraph, make.chromOrd, savepng, savepdf, saveeps, savetiff, histStack, groupedHeatmap, openHtmlPage, closeHtmlPage, multiecdf, multidensity ExportMethods: imageMap, Makesense, plotMA Package: geneRecommender Exports: gr.cv, gr.main, gr.normalize Package: GeneRegionScan Exports: exonStructure, findSequenceInGenome, getMetaprobesetsFromRegionOfInterest, getLocalMetaprobeIntensities, findProbePositions, getServerProbeIntensities, getLocalProbeIntensities, getProbesetsFromRegionOfInterest, getProbesetsFromMetaprobeset ExportMethods: getSequence, translateSampleNames, plotOnGene, excludeDoubleMatchingProbes, addSnpPdata, geneRegionScan, plotCoexpression ExportClasses: ProbeLevelSet Package: geneRxCluster Exports: critVal.alpha, critVal.power, critVal.target, gRxCluster, gRxPlot, gRxPlotClumps, gRxSummary, noprune, prune.loglik Package: GeneSelectMMD Exports: gsMMD, gsMMD.default, gsMMD2, gsMMD2.default, errRates, plotHistDensity, obtainResi Package: GeneSelector Exports: samplingcontrol ExportMethods: show, summary, toplist, plot, SelectedGenes, RankingBaldiLong, RankingEbam, RankingFC, RankingFoxDimmic, RankingLimma, RankingPermutation, RankingSam, RankingShrinkageT, RankingSoftthresholdT, RankingTstat, RankingWelchT, RankingWilcEbam, RankingWilcoxon, GenerateFoldMatrix, GenerateBootMatrix, RepeatRanking, GetStabilityOverlap, GetStabilityDistance, GetStabilityUnion, AggregateSimple, AggregatePenalty, AggregateMC, AggregateSVD, GeneSelector, HeatmapRankings, MergeRankings, MergeMethods, dispersion ExportClasses: GeneRanking, FoldMatrix, BootMatrix, RepeatedRanking, StabilityOverlap, StabilityDistance, StabilityUnion, AggregatedRanking, GeneSelectorOutput Package: geNetClassifier Exports: geNetClassifier, queryGeNetClassifier, externalValidation.stats, externalValidation.probMatrix, querySummary, calculateGenesRanking, plotExpressionProfiles, plotDiscriminantPower, plotNetwork, plotAssignments, plot.GenesRanking, plot.GeNetClassifierReturn, plot.GenesNetwork ExportMethods: initialize, show, overview, names, getSubNetwork, getNodes, getNumNodes, getEdges, getNumEdges, network2txt, getRanking, gClasses, numGenes, numSignificantGenes, getTopRanking, setProperties, genesDetails ExportClasses: GeNetClassifierReturn, GeneralizationError, GenesNetwork, GenesRanking Package: GeneticsDesign Exports: gregorius, power.casectrl, power.genotype.conti, simu.genotype.conti, GeneticPower.Quantitative.Factor, GeneticPower.Quantitative.Numeric, GPC, GPC.default Package: GeneticsPed Exports: Pedigree, as.Pedigree, is.Pedigree, generatePedigree, check, checkId, extend, family, family<-, generation, generation<-, geneContribution, isFounder, nIndividual, prune, removeIndividual, summary.Pedigree, geneFlowT, geneFlowTinv, gameteFlowM, kinship, mendelianSamplingD, inbreeding, inverseAdditive, relationshipAdditive, gpi, gpLong2Wide, hwp Package: genoCN Exports: code.genotype, genoCNA, genoCNV, plotCN Package: GenomeGraphs Exports: gdPlot, DisplayPars, geneRegionBiomart, geneBiomart, makeLegend, makeGene, makeGeneRegion, makeTranscript, makeExonArray, makeGeneModel, makeBaseTrack, makeRectangleOverlay, makeTextOverlay, makeSegmentation, makeSmoothing, makeTitle, makeGenericArray, makeIdeogram, makeGenomeAxis, makeAnnotationTrack ExportMethods: initialize, show, setPar, getPar, drawGD, showDisplayOptions, getSize, getGenomicRange ExportClasses: DisplayPars, GenericArray, MappedRead, BaseTrack, Legend, Title, Gene, Transcript, GeneModel, GenomeAxis, ExonArray, GeneRegion, TranscriptRegion, Ideogram, gdObject, Overlay, RectangleOverlay, TextOverlay, AnnotationTrack, Segmentation, TrackOverlay, Smoothing, ImplementsTrackOverlay Package: GenomeInfoDb Exports: fetchExtendedChromInfoFromUCSC, orderSeqlevels, rankSeqlevels, genomeStyles, extractSeqlevels, extractSeqlevelsByGroup, mapSeqlevels, seqlevelsInGroup, keepSeqlevels, dropSeqlevels, renameSeqlevels, restoreSeqlevels, keepStandardChromosomes, Seqinfo, GenomeDescription, summary.Seqinfo, seqinfo, seqinfo<-, seqnames, seqnames<-, seqlevels, seqlevels<-, sortSeqlevels, seqlevelsInUse, seqlevels0, seqlengths, seqlengths<-, isCircular, isCircular<-, genome, genome<-, seqlevelsStyle, seqlevelsStyle<-, seqnameStyle, seqnameStyle<-, organism, species, provider, providerVersion, releaseDate, releaseName, bsgenomeName ExportMethods: seqinfo, seqnames, seqnames<-, seqlevels, seqlevels<-, sortSeqlevels, seqlevelsInUse, seqlengths, seqlengths<-, isCircular, isCircular<-, genome, genome<-, seqlevelsStyle, seqlevelsStyle<-, seqnameStyle, seqnameStyle<-, organism, species, provider, providerVersion, releaseDate, releaseName, bsgenomeName, length, names, names<-, [, as.data.frame, show, merge, summary, intersect ExportClasses: Seqinfo, GenomeDescription Package: genomeIntervals Exports: readGff3, parseGffAttributes, getGffAttribute, GenomeIntervals, writeGff3 ExportMethods: annotation, annotation<-, seq_name, seq_name<-, strand, strand<-, inter_base, inter_base<-, type<-, [, [[, $, coerce, size, show, rank, sort, xtfrm, core_annotated, interval_union, interval_complement, interval_intersection, interval_overlap, distance_to_nearest, which_nearest ExportClasses: Genome_intervals, Genome_intervals_stranded Package: genomes ExportClasses: genomes Package: GenomicAlignments Exports: as.data.frame.OverlapEncodings, levels.OverlapEncodings, validCigar, CIGAR_OPS, explodeCigarOps, explodeCigarOpLengths, cigarToRleList, cigarRangesAlongReferenceSpace, cigarRangesAlongQuerySpace, cigarRangesAlongPairwiseSpace, extractAlignmentRangesOnReference, cigarWidthAlongReferenceSpace, cigarWidthAlongQuerySpace, cigarWidthAlongPairwiseSpace, cigarNarrow, cigarQNarrow, cigarOpTable, queryLoc2refLoc, queryLocs2refLocs, GAlignments, GAlignmentPairs, GAlignmentsList, makeGAlignmentsListFromFeatureFragments, GappedReads, findMateAlignment, findMateAlignment2, makeGAlignmentPairs, getDumpedAlignments, countDumpedAlignments, flushDumpedAlignments, readGAlignments, readGAlignmentPairs, readGAlignmentsList, readGappedReads, NATURAL_INTRON_MOTIFS, summarizeJunctions, readTopHatJunctions, readSTARJunctions, sequenceLayer, pileLettersAt, stackStringsFromBam, alphabetFrequencyFromBam, encodeOverlaps1, flipQuery, selectEncodingWithCompatibleStrand, extractQueryStartInTranscript, countCompatibleOverlaps, Union, IntersectionNotEmpty, IntersectionStrict, Lngap, Rngap, introns, rname, rname<-, cigar, qwidth, njunc, first, last, left, right, isProperPair, qseq, Loffset, Roffset, flippedQuery, Lencoding, Rencoding, Lnjunc, Rnjunc, readGAlignmentsFromBam, readGAlignmentPairsFromBam, readGAlignmentsListFromBam, readGappedReadsFromBam, junctions, qnarrow, encodeOverlaps, isCompatibleWithSplicing, isCompatibleWithSkippedExons, extractSteppedExonRanks, extractSpannedExonRanks, extractSkippedExonRanks, findCompatibleOverlaps, summarizeOverlaps, findSpliceOverlaps ExportMethods: rname, rname<-, cigar, qwidth, njunc, first, last, left, right, isProperPair, qseq, Loffset, Roffset, flippedQuery, Lencoding, Rencoding, Lnjunc, Rnjunc, readGAlignmentsFromBam, readGAlignmentPairsFromBam, readGAlignmentsListFromBam, readGappedReadsFromBam, junctions, qnarrow, encodeOverlaps, isCompatibleWithSplicing, isCompatibleWithSkippedExons, extractSteppedExonRanks, extractSpannedExonRanks, extractSkippedExonRanks, findCompatibleOverlaps, summarizeOverlaps, findSpliceOverlaps, c, start, end, width, relistToClass, ngap, narrow, coverage, pintersect, findOverlaps, countOverlaps, overlapsAny, subsetByOverlaps, map, mapCoords, seqinfo, seqinfo<-, seqnames, seqnames<-, seqlevelsInUse, granges, grglist, rglist, encoding ExportClasses: GAlignments, GAlignmentPairs, GAlignmentsList, GappedReads, OverlapEncodings Package: GenomicFeatures Exports: DEFAULT_CIRC_SEQS, makeTranscriptDb, supportedUCSCtables, supportedUCSCFeatureDbTracks, supportedUCSCFeatureDbTables, UCSCFeatureDbTableSchema, getChromInfoFromUCSC, makeTranscriptDbFromUCSC, getChromInfoFromBiomart, makeTranscriptDbFromBiomart, makeTranscriptDbFromGFF, transcripts, exons, cds, genes, disjointExons, microRNAs, tRNAs, transcriptsByOverlaps, exonsByOverlaps, cdsByOverlaps, id2name, transcriptsBy, exonsBy, cdsBy, intronsByTranscript, fiveUTRsByTranscript, threeUTRsByTranscript, extractUpstreamSeqs, extractTranscriptSeqs, transcriptLocs2refLocs, transcriptWidths, makeFeatureDbFromUCSC, makeTxDbPackage, makeTxDbPackageFromUCSC, makeTxDbPackageFromBiomart, makeFDbPackageFromUCSC, features, supportedMiRBaseBuildValues, getPromoterSeq, sortExonsByRank, extractTranscripts, extractTranscriptsFromGenome, determineDefaultSeqnameStyle ExportMethods: metadata, show, as.list, seqinfo, seqinfo<-, transcripts, exons, cds, genes, promoters, disjointExons, microRNAs, tRNAs, transcriptsByOverlaps, exonsByOverlaps, cdsByOverlaps, transcriptsBy, exonsBy, cdsBy, intronsByTranscript, fiveUTRsByTranscript, threeUTRsByTranscript, extractUpstreamSeqs, extractTranscriptSeqs, isActiveSeq, isActiveSeq<-, asBED, asGFF, getPromoterSeq, distance ExportClasses: TxDb, FeatureDb Package: GenomicFiles Exports: BamFileViews, BigWigFileViews, FaFileViews, GenomicFiles, files, files<-, reduceByFile, reduceByRange, pack, unpack, fileList, fileList<-, fileSample, fileSample<-, fileRange, fileRange<-, fileExperiment, fileExperiment<-, .fileTypeRegistry, registerFileType, findTypeRegistry, makeFileType, reduceFiles, reduceRanges, reduceByYield ExportMethods: BamFileViews, BigWigFileViews, FaFileViews, GenomicFiles, files, files<-, reduceByFile, reduceByRange, pack, unpack, [, dim, names, show, yieldSize, colData, colData<-, rowData, exptData, countBam, scanBam, summarizeOverlaps, coverage, summary ExportClasses: GenomicFiles, GenomicFileViews, BamFileViews, FaFileViews, BigWigFileViews Package: GenomicInteractions Exports: FDR<-, description<-, name<-, normalisedCount<-, pValue<-, FDR, GenomicInteractions, anchorOne, anchorTwo, annotateAnchors, annotateInteractions, annotationFeatures, calculateDistances, categoriseInteractions, count, description, export.bed12, export.bedpe, export.igraph, findOverlaps, genomeName, is.cis, is.dd, is.dt, is.pd, is.pp, is.pt, is.trans, is.tt, isInteractionType, name, normalisedCount, pValue, plotCisTrans, plotCounts, plotDists, plotInteractionAnnotations, plotRegion, plotSummaryStats, resetAnnotations, subsetByFeatures, summariseByFeatures, viewPoint, viewPointAverage ExportMethods: summariseByFeatures, sum, subsetByFeatures, show, resetAnnotations, print, plotRegion, pValue, normalisedCount, name, length, isInteractionType, is.tt, is.trans, is.pt, is.pp, is.pd, is.dt, is.dd, is.cis, genomeName, findOverlaps, export.igraph, export.bedpe, export.bed12, description, count, calculateDistances, annotationFeatures, annotateInteractions, annotateAnchors, anchorTwo, anchorOne, FDR, pValue<-, normalisedCount<-, name<-, description<-, [, FDR<- Package: GenomicRanges Exports: duplicated.GenomicRanges, sort.GenomicRanges, phicoef, makeSeqnameIds, GRanges, GRangesList, GenomicRangesList, GIntervalTree, .DollarNames.GenomicRanges, makeGRangesFromDataFrame, makeGRangesListFromFeatureFragments, tileGenome, checkConstraint, granges, grglist, rglist, SummarizedExperiment, exptData, exptData<-, rowData, rowData<-, colData, colData<-, assays, assays<-, assay, assay<- ExportMethods: checkConstraint, granges, grglist, rglist, SummarizedExperiment, exptData, exptData<-, rowData, rowData<-, colData, colData<-, assays, assays<-, assay, assay<-, length, names, names<-, dimnames<-, [, [<-, [[, [[<-, $, $<-, as.data.frame, coerce, c, cbind, rbind, show, duplicated, match, order, sort, rank, union, intersect, setdiff, start, start<-, end, end<-, width, width<-, split, unlist, range, Ops, merge, updateObject, strand, strand<-, elementMetadata, elementMetadata<-, mcols, mcols<-, values, values<-, relistToClass, splitAsListReturnedClass, compare, ranges, ranges<-, trim, ngap, score, score<-, shift, narrow, resize, flank, promoters, restrict, reduce, gaps, disjoin, isDisjoint, disjointBins, coverage, punion, pintersect, psetdiff, pgap, findOverlaps, countOverlaps, overlapsAny, subsetByOverlaps, precede, follow, nearest, distance, distanceToNearest, map, mapCoords, tile, subset, subjectHits, queryHits, seqinfo, seqinfo<-, seqnames, seqnames<- ExportClasses: Constraint, ConstraintORNULL, GenomicRanges, GenomicRangesORmissing, GRanges, GRangesList, GIntervalTree, DelegatingGenomicRanges, GenomicRangesORGRangesList, SummarizedExperiment, Assays, GenomicRangesList, SimpleGenomicRangesList Package: GenomicTuples Exports: tuples<-, GTuples, GTuplesList, IPD, duplicated.GTuples, size, tuples ExportMethods: union, tuples, tile, subsetByOverlaps, size, show, shift, setdiff, restrict, resize, replaceROWS, relistToClass, reduce, range, punion, psetdiff, promoters, pintersect, pgap, overlapsAny, order, narrow, match, mapCoords, isDisjoint, intersect, granges, gaps, flank, findOverlaps, duplicated, disjointBins, disjoin, coverage, countOverlaps, compare, c, as.data.frame, Ops, IPD, tuples<-, [<- ExportClasses: GTuplesList, GTuples Package: Genominator Exports: ExpData, aggregateExpData, applyMapped, collapseExpData, computeCoverage, getRegion, importFromAlignedReads, importToExpData, joinExpData, mergeWithAnnotation, makeGeneRepresentation, validAnnotation, computePrimingWeights, addPrimingWeights, plot.genominator.coverage, plot.genominator.goodness.of.fit, regionGoodnessOfFit, splitByAnnotation, summarizeByAnnotation, summarizeExpData, getColnames, getMode, getDBConnection, getDBFilename, getTablename, getSchema, listTables, getIndexColumns ExportMethods: initialize, show, head, $, [ ExportClasses: ExpData Package: genoset Exports: chrNames, chrNames<-, locData, locData<-, GenoSet, RleDataFrame, annotatedDataFrameFrom, baf2mbaf, boundingIndices, boundingIndicesByChr, bounds2Rle, calcGC, chr, chrIndices, chrInfo, chrOrder, cn2lr, colMeans, colSums, fixSegNAs, gcCorrect, genoPlot, genoPos, genomeAxis, isGenomeOrder, lr2cn, modeCenter, numCallable, pos, rangeColMeans, rangeMaxs, rangeMeans, rangeMins, rangeSampleMeans, rangeSegMeanLength, rangeSums, rangeWhichMaxs, rangeWhichMins, readGenoSet, rowMeans, rowSums, runCBS, segPairTable, segTable, segs2Granges, segs2Rle, segs2RleDataFrame, subsetAssayData, toGenomeOrder ExportMethods: width, start, show, sampleNames, rownames, nrow, names, genome, featureNames, end, elementLengths, dim, colnames, as.matrix, sampleNames<-, rownames<-, genome<-, featureNames<-, colnames<-, [<-, [ ExportClasses: RleDataFrame, GenoSetOrGenomicRanges, GenoSet Package: GenoView Exports: mepHuman, intSel, makeGR, plotExonRect, mutExonPlot, mepGUI, notebookVis, mepTxtInt, printOption, colSel, makePFAMObjs, updatePFAM, PFAMIDE Package: GEOquery Exports: parseGEO, parseGSM, parseGSE, parseGDS, parseGPL, getGEO, GDS2MA, GDS2eSet, getGEOfile, gunzip, getGEOSuppFiles, getGSEDataTables ExportMethods: Meta, Columns, GPLList, GSMList, Table, dataTable, Accession, show ExportClasses: GDS, GEODataTable, GEOData, GSE, GPL, GSM Package: GEOsubmission Exports: microarray2soft Package: GEWIST Exports: effectPDF, gewistLevene Package: GGBase Exports: getSS, make_smlSet, combine, dropMonomorphies, nsFilter, MAFfilter, GTFfilter, clipPCs, regressOut, combine, smList, exprs, externalize, plot_EvG, genesym, rsid, probeId, permEx, allsnps, featureNames, featureData ExportMethods: genesym, rsid, probeId, plot_EvG, permEx, clipPCs ExportClasses: smlSet, probeId, rsid Package: ggbio Exports: arrangeGrobByParsingLegend, ggbio, GGbio, scale_x_sequnit, scale_fill_giemsa, scale_fill_fold_change, circle, tracks, align.plots, alignPlots, plotFragLength, plotSpliceSum, plotStackedOverview, plotKaryogram, plotSingleChrom, plotIdeogram, Ideogram, plotGrandLinear, plotRangesLinkedToData, theme_null, theme_alignment, theme_clear, theme_tracks_sunset, theme_pack_panels, theme_noexpand, theme_genome, ggsave, zoom, zoom_in, zoom_out, nextView, prevView ExportMethods: cbind, rbind, layout_karyogram, layout_circle, stat_aggregate, stat_coverage, stat_identity, stat_mismatch, stat_stepping, stat_gene, stat_table, stat_slice, stat_bin, stat_reduce, geom_chevron, geom_arch, geom_alignment, geom_arrow, geom_arrowrect, geom_rect, geom_bar, geom_segment, autoplot, rescale, fixed, fixed<-, xlim, xlim<-, reset, backup, bgColor, bgColor<-, labeled, labeled<-, mutable, mutable<-, height, height<-, hasAxis, hasAxis<-, ggplot ExportClasses: GGbio, Ideogram, Plot, Tracked, Tracks, Grob Package: GGtools Exports: TabixFile, gwSnpTests, topSnps, eqtlTests, topFeats, getCisMap, pData, plot, best.cis.eQTLs, chromsUsed, fullreport, eqtlEstimates, probesManaged, snpsManaged, topScores, topGenes, locusNames, geneNames, geneIndcol, nthScores, vcf2sm, fdr, transScores, getBest, getAll, getCall, transTab, meqtlTests, meta.best.cis.eQTLs, meta.All.cis.eQTLs, meta.transScores, annotation, sensanal, snplocsDefault, richNull, meta.bindmaf, meta.richNull, pifdr, All.cis, collectBest, collectFiltered, cis.FDR.filter.SNPcentric, cis.FDR.filter.best, best.trans.eQTLs, chrFilter, All.cis, chrnames, chrnames<-, estimates, estimates<-, excludeRadius, excludeRadius<-, exFilter, exFilter<-, folderStem, folderStem<-, gchrpref, gchrpref<-, geneannopk, geneannopk<-, geneApply, geneApply<-, keepMapCache, keepMapCache<-, nperm, nperm<-, radius, radius<-, rhs, rhs<-, schrpref, schrpref<-, shortfac, shortfac<-, smchrpref, smchrpref<-, smFilter, smFilter<-, smpack, smpack<-, snpannopk, snpannopk<-, SSgen, SSgen<-, cis.FDR.filter.SNPcentric.complete, binqq, qqhex, gffprocess, simpleTiling, cgff2dt, ciseqByCluster, scoresCis, binnedQQ, transeqByCluster, transeqByChrom, cisScores, concatCis, eqtlTests.me, plotsens, inflammFilter, update_fdr_filt, filtgen.maf.dist, eqsens_dt, genome<-, buildConfList, add878, addgwhit, cisAssoc, sampsInVCF, appraise ExportMethods: calfig, snpchr, snpchr<-, gbufsize, gbufsize<-, batchsize, batchsize<-, extraProps, extraProps<-, chrnames, chrnames<-, estimates, estimates<-, excludeRadius, excludeRadius<-, exFilter, exFilter<-, folderStem, folderStem<-, gchrpref, gchrpref<-, geneannopk, geneannopk<-, geneApply, geneApply<-, keepMapCache, keepMapCache<-, nperm, nperm<-, radius, radius<-, rhs, rhs<-, schrpref, schrpref<-, shortfac, shortfac<-, smchrpref, smchrpref<-, smFilter, smFilter<-, smpack, smpack<-, snpannopk, snpannopk<-, SSgen, SSgen<-, gwSnpTests, show, topFeats, plot, transTab ExportClasses: EqAppr, eqtlTestsManager, eqtlEstimatesManager, mcwBestCis, gwSnpScreenResult, transManager, allSigCis, sensiCisInput, sensiCisOutput, mcwAllCis, cisRun, CisConfig, TransConfig Package: girafe Exports: AlignedGenomeIntervals, plotAligned, trimAdapter, perWindow, fracOverlap, intPhred, coverageOneStrand, addNBSignificance, plotNegBinomFit, medianByPosition, agiFromBam, getFeatureCounts, countReadsAnnotated, chrlengths, clusters, coerce, organism, plot, sample, subset, summary ExportMethods: plot, [, interval_overlap, interval_included, chrlengths, chrlengths<-, chromosome, coerce, coverage, clusters, detail, export, extend, hist, nchar, matches, matches<-, id, id<-, organism, organism<-, reads, reads<-, reduce, sample, score, score<-, seq_name, show, sort, strand, strand<-, subset, summary, width, which_nearest ExportClasses: AlignedGenomeIntervals Package: GlobalAncova Exports: GAGO, GAKEGG, GABroad, GlobalAncova.decomp, pair.compare, Plot.sequential, Plot.all ExportMethods: GlobalAncova, GlobalAncova.closed, Plot.genes, Plot.subjects Package: globaltest Exports: gt, mlogit, gtGO, combine, leafNodes, draw, gtKEGG, gtBroad, gtConcept, comparative, focusLevel, inheritance, covariates, features, subjects, gt.options, findFocus, gtPS, gtKS, gtLI, bbase, btensor, reparamZ, reweighZ ExportMethods: [, [[, show, result, p.value, length, names, names<-, sort, size, hist, z.score, summary, residuals, fitted.values, coefficients, alias, alias<-, model.matrix, weights, p.adjust, subsets, extract, sterms ExportClasses: mlogit, gt.object Package: gmapR Exports: bam_tally, GmapGenome, GmapGenomeDirectory, GsnapParam, directory, BamTallyParam, makeGmapGenomePackage, GsnapOutput, GmapSnps, GmapSnpDirectory, TP53Genome, TP53Which, variantSummary ExportMethods: bamPaths, path, genome, seqinfo, gsnap, snps<-, spliceSites<-, getSeq ExportClasses: GmapGenome, GmapGenomeDirectory, GmapSnpDirectory, GsnapOutput, GmapSnps, BamTallyParam, GsnapParam Package: GOexpress Exports: cluster_GO, expression_plot, expression_plot_symbol, expression_profiles, expression_profiles_symbol, GO_analyse, heatmap_GO, hist_scores, list_genes, overlap_GO, plot_design, quantiles_scores, rerank, subEset, subset_scores, table_genes Package: GOFunction Exports: GOFunction Package: goProfiles Exports: basicProfile, expandedProfile, GOTermsList, getAncestorsLst, getGOLevel, compSummary, equivSummary, fitGOProfile, compareGOProfiles, compareProfilesLists, compareGeneLists, plotProfiles, printProfiles, mergeProfilesLists, as.GOTerms.frame, as.GOTerms.list, BioCpack2EntrezIDS, BioCpack2Profiles, BioCprobes2Entrez, GOTermsFrame2GOTermsList, expandTerm, expandedLevel, equivalentGOProfiles, ngenes, fisherGOProfiles, contractedProfile Package: GOSemSim Exports: clusterSim, combineScores, geneSim, getDb, getSupported_Org, goSim, loadGOMap, mclusterSim, mgeneSim, mgoSim, termSim Package: goseq Exports: getgo, getlength, goseq, makespline, nullp, plotPWF Package: GOSim Exports: getOffsprings, getAncestors, getParents, getChildren, setEvidenceLevel, setOntology, getGOInfo, filterGO, getGeneSim, getGeneFeaturesPrototypes, getGeneSimPrototypes, selectPrototypes, setEnrichmentFactors, getGOGraph, getGOGraphsGenes, calcICs, getMinimumSubsumer, getDisjCommAnc, getTermSim, evaluateClustering, GOenrichment, getGeneFeatures, calc.diffusion.kernel, load.diffusion.kernel Package: GOstats Exports: compCorrGraph, compGdist, enumPairs, GOGraph, idx2dimnames, isTriad, makeGOGraph, notConn, oneGOGraph, reduce2Degreek, shortestPath, simLL, simLP, simUI, triadCensus, probeSetSummary, termGraphs, inducedTermGraph, plotGOTermGraph ExportMethods: hyperGTest, pvalues, description, oddsRatios, expectedCounts, htmlReport, goDag, geneCounts, universeCounts, geneIds, geneIdUniverse, universeMappedCount, geneMappedCount, annotation, testName, summary ExportClasses: GOHyperGResult Package: GOsummaries Exports: add_expression.gosummaries, add_to_slot.gosummaries, customize, gosummaries, is.gosummaries, panel_boxplot, panel_boxplot_classes, panel_violin, panel_violin_box, panel_violin_box_classes, panel_violin_classes, plotWordcloud Package: GOTHiC Exports: pairReads, mapReadsToRestrictionSites, GOTHiC Package: gpls Exports: gpls, glpls1a, glpls1a.cv.error, glpls1a.train.test.error, glpls1a.mlogit, glpls1a.logit.all, glpls1a.mlogit.cv.error Package: graph Exports: graphNEL, graphAM, boundary, buildRepDepGraph, calcProb, calcSumProb, duplicatedEdges, graph2SparseM, listEdges, randomEGraph, randomGraph, randomNodeGraph, validGraph, eWV, pathWeights, .dropEdges, aveNumEdges, sparseM2Graph, gxlTreeNEL, ftM2adjM, ftM2graphNEL, .ftM2other, int2ftM, ftM2int, aM2bpG, mostEdges, numNoEdges, reverseEdgeDirections, ugraphOld, graph.par, graph.par.get, graphRenderInfo, nodeRenderInfo, edgeRenderInfo, parRenderInfo, nodeRenderInfo<-, edgeRenderInfo<-, parRenderInfo<-, graphRenderInfo<-, graphBAM, MultiGraph, eweights, edgeSetIntersect0, edgeSetUnion0, extractFromTo, subsetEdgeSets, extractGraphAM, extractGraphBAM, mgEdgeData, mgEdgeData<- ExportMethods: DFS, Dist, acc, addEdge, addNode, adj, adjacencyMatrix, clearNode, clusteringCoefficient, combineNodes, complement, connComp, degree, dumpGXL, edgeL, edgeMatrix, edgeNames, edgeWeights, edgemode, edgemode<-, edges, nodes<-, fromGXL, inEdges, initialize, intersection, intersection2, isAdjacent, isConnected, isDirected, join, nodes, numNodes, numEdges, plot, removeEdge, removeNode, show, subGraph, threshold, toGXL, union, validateGXL, coerce, toDotR, attrDefaults, attrDefaults<-, edgeDataDefaults, edgeDataDefaults<-, mgEdgeDataDefaults, mgEdgeDataDefaults<-, nodeDataDefaults, nodeDataDefaults<-, edgeData, edgeData<-, nodeData, nodeData<-, attrDataItem, attrDataItem<-, removeAttrDataItem<-, ugraph, leaves, updateGraph, extractFromTo, graphIntersect, graphUnion, removeEdgesByWeight, edgeSets ExportClasses: distGraph, clusterGraph, graph, graphNEL, file, connection, gzfile, bzfile, url, graphAM, attrData, simpleEdge, edgeSet, edgeSetNEL, edgeSetAM, multiGraph, renderInfo, MultiGraph, graphBAM, graphBase Package: GraphAlignment Exports: LinearAssignment, ComputeM, AlignNetworks, CreateScoreMatrix, InvertPermutation, Permute, Trace, InitialAlignment, GetBinNumber, VectorToBin, MatrixToBin, ComputeScores, GenerateExample, ComputeLinkParameters, ComputeNodeParameters, EncodeDirectedGraph, AnalyzeAlignment, AlignedPairs, .Last.lib Package: GraphAT Exports: clust2Mat, getpvalue, makeClustM, mat2UndirG, permEdgesM2M, permNodesM2M, permPower Package: graphite Exports: convertIdentifiers, pathwayGraph, cytoscapePlot, prepareSPIA, runSPIA, runDEGraph, runDEGraphMulti, runTopologyGSA, runTopologyGSAMulti, runClipper, runClipperMulti ExportMethods: show, nodes, edges ExportClasses: pathway Package: GraphPAC Exports: Find.TSP.Path, GraphClust, Plot.Protein Package: groHMM Exports: writeWiggle, detectTranscripts, makeConsensusAnnotations, evaluateHMMInAnnotations, windowAnalysis, breakTranscriptsOnGenes, combineTranscripts, getTxDensity, limitToXkb, runMetaGene, metaGene, pausingIndex, polymeraseWave, getCores Package: GSAR Exports: HDP.ranking, WWtest, KStest, RKStest, GSNCAtest, findMST2, plotMST2.pathway Package: GSCA Exports: GSCAplot, GSCA, GSCAeda, annotatePeaks, tabSearch, ConstructTG, GSCAui Package: GSEABase Exports: NullIdentifier, ENSEMBLIdentifier, EnzymeIdentifier, GenenameIdentifier, RefseqIdentifier, SymbolIdentifier, UnigeneIdentifier, UniprotIdentifier, EntrezIdentifier, AnnotationIdentifier, AnnoOrEntrezIdentifier, GOAllFrameIdentifier, NullCollection, ExpressionSetCollection, ComputedCollection, KEGGCollection, OMIMCollection, PMIDCollection, ChrCollection, ChrlocCollection, MapCollection, PfamCollection, PrositeCollection, GOCollection, OBOCollection, BroadCollection, asBroadUri, getBroadSets, toBroadXML, getGmt, toGmt, getOBOCollection, geneIds, geneIds<-, ontology ExportMethods: show, coerce, details, initialize, intersect, union, setdiff, &, |, Logic, incidence, mapIdentifiers, annotation, annotation<-, ids, bcCategory, bcSubCategory, evidenceCode, ontology, subsets, goSlim, GeneSet, geneIdType, geneIds, setIdentifier, setName, description, longDescription, organism, pubMedIds, urls, contributor, setVersion, creationDate, collectionType, geneIdType<-, geneIds<-, setIdentifier<-, setName<-, description<-, longDescription<-, organism<-, pubMedIds<-, urls<-, contributor<-, setVersion<-, creationDate<-, collectionType<-, GeneColorSet, phenotype, geneColor, phenotypeColor, coloring, phenotype<-, geneColor<-, phenotypeColor<-, coloring<-, GeneSetCollection, updateObject, names, [, [[ ExportClasses: GeneIdentifierType, NullIdentifier, AnnotationIdentifier, ENSEMBLIdentifier, EntrezIdentifier, EnzymeIdentifier, GenenameIdentifier, RefseqIdentifier, SymbolIdentifier, UnigeneIdentifier, UniprotIdentifier, GOAllFrameIdentifier, CollectionType, NullCollection, ExpressionSetCollection, ComputedCollection, CollectionIdType, KEGGCollection, OMIMCollection, PMIDCollection, ChrCollection, ChrlocCollection, MapCollection, PfamCollection, PrositeCollection, GOCollection, OBOCollection, BroadCollection, GeneSet, GeneColorSet, GeneSetCollection Package: GSEAlm Exports: lmPerGene, gsealmPerm, resplot, restrip, CooksDPerGene, dfbetasPerGene, dffitsPerGene, Leverage, getResidPerGene, mnDiffPlot, GSNormalize, identity, one Package: GSReg Exports: GSReg.GeneSets.EVA, GSReg.GeneSets.DIRAC Package: GSRI Exports: rowt, rowF ExportMethods: gsri, getGsri, getCdf, getParms, export, show, summary, plot, readCls, readGct, sortGsri ExportClasses: Gsri Package: GSVA ExportMethods: gsva, filterGeneSets, computeGeneSetsOverlap Package: Gviz Exports: .chrName, .doCache, AlignedReadTrack, AlignmentsTrack, AnnotationTrack, DetailsAnnotationTrack, BiomartGeneRegionTrack, CustomTrack, DataTrack, DisplayPars, SequenceTrack, OverlayTrack, drawGD, GeneRegionTrack, GenomeAxisTrack, HighlightTrack, IdeogramTrack, UcscTrack, addScheme, as.list, availableDefaultMapping, availableDisplayPars, clearSessionCache, exportTracks, getScheme, plotTracks ExportMethods: [, as.list, chromosome, chromosome<-, coerce, consolidateTrack, coords, coverage, displayPars, displayPars<-, end, end<-, exon, exon<-, feature, feature<-, gene, gene<-, genome, genome<-, getPar, group, group<-, head, identifier, identifier<-, imageMap, initialize, length, max, min, names, names<-, position, range, ranges, score, seqnames, seqlevels, seqinfo, setPar, split, stacking, stacking<-, stacks, start, start<-, strand, strand<-, subseq, subset, symbol, symbol<-, tags, tail, transcript, transcript<-, values, values<-, width, width<- ExportClasses: AlignedReadTrack, AlignmentsTrack, AnnotationTrack, DetailsAnnotationTrack, BiomartGeneRegionTrack, DataTrack, DisplayPars, GdObject, GeneRegionTrack, GenomeAxisTrack, IdeogramTrack, ImageMap, NumericTrack, RangeTrack, SequenceTrack, StackedTrack, HighlightTrack, OverlayTrack, CustomTrack Package: gwascat Exports: impute.snps, locs4trait, topTraits, elementMetadata, ranges, chklocs, riskyAlleleCount, getRsids, getTraits, subsetByChromosome, subsetByTraits, obo2graphNEL, makeCurrentGwascat, traitsManh, gwcex2gviz, values, mcols, mcols<-, seqnames, match, overlapsAny, DataFrame, bindcadd_snv, show ExportMethods: getRsids, [, getTraits, subsetByChromosome, subsetByTraits, show ExportClasses: gwaswloc, SnpMatrix Package: GWASTools Exports: SnpAnnotationDataFrame, SnpAnnotationSQLite, ScanAnnotationDataFrame, ScanAnnotationSQLite, NcdfReader, NcdfGenotypeReader, NcdfIntensityReader, GdsReader, GdsGenotypeReader, GdsIntensityReader, MatrixGenotypeReader, GenotypeData, IntensityData, alleleFrequency, anomSegmentBAF, anomFilterBAF, anomDetectBAF, anomDetectLOH, anomIdentifyLowQuality, anomSegStats, anomStatsPlot, apartSnpSelection, asSnpMatrix, assocTestCPH, assocTestFisherExact, assocTestRegression, BAFfromClusterMeans, BAFfromGenotypes, batchChisqTest, batchFisherTest, checkGenotypeFile, checkImputedDosageFile, checkIntensityFile, checkNcdfGds, chromIntensityPlot, convertGdsNcdf, convertNcdfGds, convertVcfGds, createDataFile, createAffyIntensityFile, duplicateDiscordance, duplicateDiscordanceAcrossDatasets, duplicateDiscordanceProbability, findBAFvariance, gdsImputedDosage, gdsCheckImputedDosage, gdsSetMissingGenotypes, gdsSubset, gdsSubsetCheck, genoClusterPlot, genoClusterPlotByBatch, genotypeToCharacter, gwasExactHW, hetByScanChrom, hetBySnpSex, ibdAreasDraw, ibdAssignRelatedness, ibdAssignRelatednessKing, ibdPlot, imputedDosageFile, intensityOutliersPlot, manhattanPlot, meanIntensityByScanChrom, meanSdByChromWindow, medianSdOverAutosomes, mendelErr, mendelList, mendelListAsDataFrame, minorAlleleDetectionAccuracy, missingGenotypeByScanChrom, missingGenotypeBySnpSex, ncdfAddData, ncdfAddIntensity, ncdfCheckGenotype, ncdfCheckIntensity, ncdfCreate, ncdfImputedDosage, ncdfSetMissingGenotypes, ncdfSubset, ncdfSubsetCheck, pedigreeCheck, pedigreeDeleteDuplicates, pedigreeMaxUnrelated, pedigreePairwiseRelatedness, pasteSorted, plinkCheck, plinkToNcdf, plinkWrite, pseudoautoIntensityPlot, qqPlot, qualityScoreByScan, qualityScoreBySnp, sdByScanChromWindow, setMissingGenotypes, simulateGenotypeMatrix, simulateIntensityMatrix, snpCorrelationPlot, vcfCheck, vcfWrite, allequal, getobj, saveas, readWriteFirst ExportMethods: getAlleleA, getAlleleB, getAnnotation, getAttribute, getBAlleleFreq, getChromosome, getDimension, getDimensionNames, getGenotype, getLogRRatio, getMetadata, getNodeDescription, getPosition, getQuality, getQuery, getScanID, getScanVariable, getScanVariableNames, getSex, getSnpID, getSnpVariable, getSnpVariableNames, getVariable, getVariableNames, getX, getY, hasBAlleleFreq, hasCoordVariable, hasLogRRatio, hasQuality, hasScanAnnotation, hasScanVariable, hasSex, hasSnpAnnotation, hasSnpVariable, hasVariable, hasX, hasY, nsnp, nscan, writeAnnotation, writeMetadata, autosomeCode, XchromCode, YchromCode, XYchromCode, MchromCode, open, close, show ExportClasses: SnpAnnotationDataFrame, SnpAnnotationSQLite, ScanAnnotationDataFrame, ScanAnnotationSQLite, NcdfReader, NcdfGenotypeReader, NcdfIntensityReader, GdsReader, GdsGenotypeReader, GdsIntensityReader, MatrixGenotypeReader, GenotypeData, IntensityData Package: hapFabia Exports: makePipelineFile, hapFabiaVersion, findDenseRegions, matrixPlot, plotIBDsegment, sim, iterateIntervals, identifyDuplicates, analyzeIBDsegments, hapFabia, simulateIBDsegments, split_sparse_matrix, vcftoFABIA, simulateIBDsegmentsFabia, IBDsegmentList, IBDsegment ExportMethods: plot, summary, [[, [[<-, [, [<-, topLZ, plotL, histL, extractIBDsegments, ID, ID<-, bicluster_id, bicluster_id<-, chromosome, chromosome<-, IBDsegmentPos, IBDsegmentPos<-, IBDsegmentLength, IBDsegmentLength<-, numberIndividuals, numberIndividuals<-, numbertagSNVs, numbertagSNVs<-, individuals, individuals<-, tagSNVs, tagSNVs<-, populationIndividuals, populationIndividuals<-, idIndividuals, idIndividuals<-, labelIndividuals, labelIndividuals<-, platformIndividuals, platformIndividuals<-, coreClusterIndividuals, coreClusterIndividuals<-, tagSNVPositions, tagSNVPositions<-, tagSNVAlleles, tagSNVAlleles<-, tagSNVNames, tagSNVNames<-, tagSNVFreq, tagSNVFreq<-, tagSNVGroupFreq, tagSNVGroupFreq<-, tagSNVChange, tagSNVChange<-, tagSNVsPerIndividual, tagSNVsPerIndividual<-, individualPerTagSNV, individualPerTagSNV<-, tagSNVAnno, tagSNVAnno<-, IBDsegments, IBDsegments<-, lengthList, lengthList<-, statistics, statistics<-, setAnnotation, setStatistics, compareIBDsegmentLists, mergeIBDsegmentLists, IBDsegmentList2excel, plotLarger ExportClasses: IBDsegment, IBDsegmentList Package: Harshlight Exports: HarshComp, HarshExt, Harshlight Package: HDTD Exports: centerdata, covmat.hat, covmat.ts, meanmat.hat, meanmat.ts, orderdata ExportMethods: print.covmat.hat, print.covmat.ts, print.meanmat.hat, print.meanmat.ts ExportClasses: covman.hat, covmat.ts, meanmat.hat, meanmat.ts Package: Heatplus Exports: heatmap_2, heatmap_plus, RainbowPastel, RGBColVec, oldCutplot.dendrogram, oldPicketplot, convAnnData, picketPlot, annHeatmap2, regHeatmap, annHeatmap, annHeatmap.default, regHeatmap.default, plot.annHeatmap, g2r.colors, heatmapLayout, picketPlot, niceBreaks, breakColors, doLegend, print.annHeatmap, extractArg, modifyExistingList, annHeatmap.ExpressionSet Package: HELP Exports: readSampleKey ExportMethods: calcGC, calcPrototype, calcTm, combineData, createWiggle, exprs2, exprs2<-, fuzzyMatches, getFeatures, getSamples, plotBins, plotChip, plotFeature, plotPairs, quantileNormalize, readDesign, readPairs Package: HEM Exports: am.tran, am.tran.half, base.ASE.Olig, base.error.Olig, base.error.Olig.quanOnly, base.PSE.Olig, boot.base.ASE.Olig, boot.base.error.Olig, boot.base.PSE.Olig, fixbound.predict.smooth.spline, hem, hem.eb.prior, hem.fdr, hem.null.no, hem.null.one, hem.null.two, hem.preproc, nonpar.error.Olig, nonpar.no.error.Olig, nonpar.rep.error.Olig, par.error.Olig, par.no.error.Olig, par.rep.error.Olig, permut, quant.normal, quant.normal2, remove.sig.genes Package: hiAnnotator Exports: cleanColname, doAnnotation, get2NearestFeature, getFeatureCounts, getFeatureCountsBig, getLowestDists, getNearestFeature, getRelevantCol, getSitesInFeature, getUCSCtable, getWindowLabel, makeChunks, makeGRanges, makeUCSCsession, plotdisFeature Package: HilbertVis Exports: hilbertCurve, hilbertCurvePoint, plotHilbertCurve, shrinkVector, plotLongVector, makeWiggleVector, hilbertImage, makeRandomTestData, showHilbertImage Package: HilbertVisGUI Exports: simpleLinPlot, hilbertDisplay, hilbertDisplayThreeChannel, dotsapply Package: hiReadsProcessor Exports: addFeature, addListNameToReads, annotateSites, blatListedSet, blatSeqs, chunkize, clusterSites, crossOverCheck, decodeByBarcode, dereplicateReads, doRCtest, extractFeature, extractSeqs, findAndRemoveVector, findAndTrimSeq, findBarcodes, findIntegrations, findLTRs, findLinkers, findPrimers, findVector, getIntegrationSites, getSectorsForSamples, getSonicAbund, isuSites, otuSites, pairUpAlignments, pairwiseAlignSeqs, primerIDAlignSeqs, pslCols, pslToRangedObject, read.BAMasPSL, read.SeqFolder, read.blast8, read.psl, read.sampleInfo, read.seqsFromSector, removeReadsWithNs, replicateReads, sampleSummary, splitByBarcode, splitSeqsToFiles, startgfServer, trimSeqs, troubleshootLinkers, vpairwiseAlignSeqs, write.listedDNAStringSet, write.psl Package: HiTC Exports: binningC, CQC, intervalsDist, discretize, exportC, export.my5C, importC, import.my5C, extractRegion, getExpectedCounts, getAnnotatedRestrictionSites, getRestrictionFragmentsPerChromosome, HTCexp, HTClist, normLGF, normICE, pca.hic, removeIntervals, setIntervalScale, setGenomicFeatures, summary ExportMethods: as.list, c, detail, show, intdata, intdata<-, isBinned, isIntraChrom, isSymmetric, y_intervals, y_intervals<-, x_intervals, x_intervals<-, xy_intervals, id, forcePairwise, forceSymmetric, isPairwise, isComplete, mapC, plot, normPerReads, normPerExpected, normPerTrans, range, ranges, seqlevels, substract, divide ExportClasses: HTCexp, HTClist Package: HMMcopy Exports: wigsToRangedData, correctReadcount, plotBias, plotCorrection, wigToRangedData, wigToArray, rangedDataToWig, rangedDataToSeg, HMMsegment, plotSegments, plotParam, stateCols Package: hopach Exports: boot2fuzzy, bootplot, bootmedoids, boothopach, dplot, vdisscosangle, vdissabscosangle, vdisseuclid, vdissabseuclid, vdisscor, vdissabscor, distancematrix, distancevector, dissvector, dissmatrix, vectmatrix, correlationordering, improveordering, disseuclid, disscor, dissabscor, disscosangle, dissabscosangle, makeTree, hopach2tree, labelstomss, silcheck, msscheck, digits, cutdigits, cutzeros, nonzeros, msssplitcluster, mssnextlevel, orderelements, mssinitlevel, paircoll, collap, msscollap, mssmulticollap, mssrundown, msscomplete, newnextlevel, newsplitcluster, hopach, makeoutput, prune, is.hdist, hdist ExportMethods: show, [, coerce, as.matrix, as.hdist, as.vector, length ExportClasses: hdist Package: hpar Exports: getHpaVersion, getHpaDate, getHpaEnsembl, getHpa, getHparOptions, setHparOptions Package: HTqPCR Exports: cbind.qPCRset, changeCtLayout, clusterCt, filterCategory, filterCtData, getCt, getCtHistory, heatmapSig, limmaCtData, mannwhitneyCtData, n.samples, n.wells, normalizeCtData, plotCtArray, plotCtBoxes, plotCtCategory, plotCtCor, plotCtDensity, plotCtHeatmap, plotCtHistogram, plotCtOverview, plotCtPCA, plotCtReps, plotCtRQ, plotCtScatter, plotCtSignificance, plotCtVariation, plotCVBoxes, plotCtLines, plotCtCard, rbind.qPCRset, readCtData, setCategory, setCt<-, setCtHistory<-, ttestCtData, plotCtPairs ExportMethods: [, exprs, exprs<-, featureCategory, featureCategory<-, featureClass, featureClass<-, featureNames, featureNames<-, featurePos, featurePos<-, featureType, featureType<-, flag, flag<-, sampleNames, sampleNames<-, show, summary ExportClasses: qPCRset Package: HTSanalyzeR Exports: aggregatePvals, annotationConvertor, biogridDataDownload, celAnnotationConvertor, cellHTS2OutputStatTests, collectionGsea, drosoAnnotationConvertor, duplicateRemover, FDRcollectionGsea, analyzeGeneSetCollections, GOGeneSets, gseaPlots, gseaScores, gseaScoresBatch, gseaScoresBatchParallel, HTSanalyzeR4cellHTS2, KeggGeneSets, mammalAnnotationConvertor, multiHyperGeoTest, networkAnalysis, networkPlot, pairwiseGsea, pairwiseGseaPlot, pairwisePhenoMannWhit, permutationPvalueCollectionGsea, hyperGeoTest, writeReportHTSA, changes ExportMethods: analyze, reportAll, plotSubNet, viewSubNet, viewEnrichMap, plotEnrichMap, plotGSEA, viewGSEA, writeHits, getTopGeneSets, appendGSTerms, interactome, preprocess, show, summarize, report ExportClasses: GSCA, NWA Package: HTSeqGenie Exports: FastQStreamer.getReads, FastQStreamer.init, FastQStreamer.release, TP53GenomicFeatures, alignReads, analyzeVariants, bamCountUniqueReads, buildConfig, buildGenomicFeaturesFromTxDb, buildTP53FastaGenome, calculateCoverage, calculateTargetLengths, checkConfig, checkGATKJar, checkPicardJar, computeBamStats, computeCoverage, consolidateByRead, countGenomicFeatures, countGenomicFeaturesChunk, detectAdapterContam, detectQualityInFASTQFile, detectRRNA, filterByLength, filterQuality, findVariantFile, gatk, getBams, getChunkDirs, getConfig, getConfig.integer, getConfig.logical, getConfig.numeric, getConfig.vector, getEndNumber, getMemoryUsage, getNumberOfReadsInFASTQFile, getNumericVectorDataFromFile, getObjectFilename, getPackageFile, getRRNAIds, getTabDataFromFile, getTraceback, hashCoverage, hashVariants, hashVector, initDirs, initLog, initLogger, initPipelineFromConfig, initPipelineFromSaveDir, isAboveQualityThresh, isAdapter, isConfig, listIterator.init, listIterator.next, loadConfig, logdebug, logerror, loginfo, logwarn, makeDir, markDuplicates, markDups, mergeAlignReads, mergeCoverage, mergeLanes, mergePreprocessReads, mergeSummaryAlignment, parseDCF, parseSummaries, plotDF, preprocessReads, processChunks, readInputFiles, readRNASeqEnds, realignIndels, relativeBarPlot, removeChunkDir, resource, rpkm, runAlignment, runPipeline, runPipelineConfig, runPreprocessReads, safe.yield, safeExecute, safeGetObject, safeUnlink, saveWithID, sclapply, setUpDirs, setupTestFramework, statCountFeatures, traceMem, trimReads, trimTailsByQuality, truncateReads, tryKeepTraceback, updateConfig, vcfStat, wrap.callVariants, writeAudit, writeConfig, writeFastQFiles, writeFeatureCountsHTML, writeGenomicFeaturesReport, writePreprocessAlignReport, writeSummary, writeVCF Package: htSeqTools Exports: fdrEnrichedCounts, gridCoverage, plotChrRegions, coverageDiff, rowLogRegLRT, plotminHeight ExportMethods: alignPeaks, extendRanges, filterDuplReads, mergeRegions, enrichedRegions, enrichedPeaks, stdPeakLocation, PeakLocation, listOverlap, tabDuplReads, cmds, cmdsFit, islandCounts, ssdCoverage, giniCoverage, regionsCoverage, stdGrid, plot, lines, enrichedChrRegions, countHitsWindow, getViewsInfo, getCover, plotMeanCoverage, findPeakHeight ExportClasses: cmdsFit, gridCover Package: HTSFilter Exports: normalizeData ExportMethods: HTSBasicFilter, HTSFilter Package: HybridMTest Exports: hybrid.test, row.oneway.anova, row.kruskal.wallis, row.kgrp.shapiro, row.kgrp.shapiro, row.pearson, row.spearman, row.slr.shapiro, grenander.ebp Package: hyperdraw ExportMethods: graphBPH, plot, graphLayout, edgeDataDefaults<-, edgeData<-, nodeDataDefaults<-, nodeData<-, graphDataDefaults<-, graphData<- ExportClasses: graphBPH, RagraphBPH Package: hypergraph Exports: kCoresHypergraph, vCoverHypergraph, Hypergraph, Hyperedge, DirectedHyperedge, l2hel ExportMethods: nodes, label, label<-, show, toUndirected, head, tail, hyperedges, numNodes, inciMat, inciMat2HG, initialize, toGraphNEL, hyperedgeLabels ExportClasses: Hypergraph, Hyperedge, DirectedHyperedge Package: iASeq Exports: ASErawfit, iASeqmotif, singleEMfit, plotBIC, plotMotif Package: iBBiG Exports: iBBiG, makeArtificial, makeSimDesignMat ExportMethods: plot, show, summary, RowScorexNumber, Clusterscores, Seeddata, Parameters, RowxNumber, NumberxCol, Number, info, analyzeClust, JIdist ExportClasses: iBBiG Package: iBMQ Exports: calculateThreshold, eqtlClassifier, eqtlFinder, eqtlMcmc, hotspotFinder Package: Icens Exports: Bisect, BVcliques, BVclmat, BVmacprod, BVsupport, EM, EMICM, EMICMmac, Intersection, ISDM, Maclist, Macmat, MLEintvl, PGM, Plotboxes, PMGA, rescaleP, Subset, VEM, VEMICMmac Package: iChip Exports: iChip1, iChip2, enrichreg, lmtstat Package: iClusterPlus Exports: compute.pod, plotiCluster, iCluster, iCluster2, tune.iCluster2, iClusterPlus, tune.iClusterPlus, plotHeatmap, getBIC, getDevR, getClusters, CNregions, iManual Package: idiogram Exports: .usedChromExprs, .rwb ExportClasses: cytoband Package: IdMappingAnalysis Exports: plot.Bootstrap, plot.Corr, plot.CorrData, examples, merge.IdMap, as.list.IdMap, as.data.frame.IdMapBase, dim.IdMapBase, dimnames.IdMapBase, getName.IdMapBase, [.IdMapBase, plot.IdMapCounts, summary.IdMapDiffCounts, plot.IdMapDiffCounts, as.data.frame.JointIdMap, boxplot.JointUniquePairs, plot.Mixture, unique.UniquePairs, Bootstrap, Corr, CorrData, DataFilter, Display, IdMap, IdMapBase, IdMapCounts, IdMapDiff, IdMapDiffCounts, JointIdMap, JointUniquePairs, Misc, Mixture, Subset, UniquePairs, aligned, as.IdMap, as.MultiSet, as.UniquePairs, byColNames, byColumn, byRow, byRowNames, clust, copy, corr.boxplot, corr.plot, create, CsvList.merge, diffCounts.plot, do.apply, do.glm, ecdf.plot, fisherTransform, fisherTransformInverse, fisherTransformJacobean, getBootstrap, getCompoundEvents, getCompoundGroups, getCorr, getCorrData, getCorrDataFrame, getCounts, getData, getDiff, getExperimentSet, getIdMapList, getMapNames, getMatch, getMatchInfo, getMixture, getSampleNames, getStats, getUnionIdMap, getUniquePairs, interactive.corr.boxplot, interactive.corr.plot, interactive.mixture.boxplot, interactive.mixture.plot, interactive.plot, interleave, line.loess, line.unsorted, minAvgCountConstraint, minCountConstraint, minCountGroupConstraint, mixture.boxplot, mixture.plot, pack.experiments, primaryIDs, primaryKey, progressMsg, removeNASeries, secondaryKey, subsetCorr, subsetData, subsetGroups, swapKeys, textBoundingBox, to.base, to.binary.logical, to.index.expr, words, zoom.pars, aligned.IdMapBase, as.IdMap.UniquePairs, as.MultiSet.CorrData, as.UniquePairs.IdMap, byColNames.Subset, byColumn.Subset, byRow.Subset, byRowNames.Subset, clust.Mixture, copy.Display, corr.boxplot.JointUniquePairs, corr.plot.JointUniquePairs, create.Display, create.UniquePairs, CsvList.merge.Misc, diffCounts.plot.JointIdMap, do.apply.DataFilter, do.glm.JointUniquePairs, ecdf.plot.JointIdMap, expectedUtility, fisherTransform.DataFilter, fisherTransformInverse.DataFilter, fisherTransformJacobean.DataFilter, fit2clusters, getBootstrap.JointUniquePairs, getCompoundEvents.IdMapDiffCounts, getCompoundGroups.IdMapDiffCounts, getCorr.JointUniquePairs, getCorrData.JointUniquePairs, getCorrDataFrame.JointUniquePairs, getCounts.IdMap, getCounts.JointIdMap, getData.Corr, getData.Mixture, getDiff.JointIdMap, getExperimentSet.CorrData, getIdMapList.JointIdMap, getMapNames.JointIdMap, getMapNames.JointUniquePairs, getMatch.UniquePairs, getMatchInfo.JointIdMap, getMatchInfo.JointUniquePairs, getMixture.JointUniquePairs, getSampleNames.CorrData, getStats.IdMapCounts, getStats.Mixture, getUnionIdMap.JointIdMap, getUniquePairs.Corr, getUniquePairs.CorrData, getUniquePairs.JointUniquePairs, interactive.corr.boxplot.JointUniquePairs, interactive.corr.plot.JointUniquePairs, interactive.mixture.boxplot.JointUniquePairs, interactive.mixture.plot.JointUniquePairs, interactive.plot.CorrData, interactive.plot.JointUniquePairs, interleave.Misc, line.loess.Display, line.unsorted.Display, logTen, logTen.DataFilter, minAvgCountConstraint.DataFilter, minCountConstraint.DataFilter, minCountGroupConstraint.DataFilter, mixture.boxplot.JointUniquePairs, mixture.plot.JointUniquePairs, pack.experiments.CorrData, primaryIDs.IdMapBase, primaryKey.CorrData, primaryKey.IdMapBase, primaryKey.Mixture, progressMsg.Display, removeNASeries.DataFilter, secondaryKey.CorrData, secondaryKey.IdMapBase, secondaryKey.Mixture, subsetCorr.JointUniquePairs, subsetData.JointUniquePairs, subsetGroups.JointUniquePairs, swapKeys.IdMap, swapKeys.UniquePairs, textBoundingBox.Display, to.base.Misc, to.binary.logical.Misc, to.index.expr.Misc, words.Misc, zoom.pars.Display Package: IdMappingRetrieval Exports: Annotation, AnnotationAffx, AnnotationDavid, AnnotationDavidCsv, AnnotationEnsembl, AnnotationEnsemblCsv, AnnotationEnvision, AnnotationNetAffx, ServiceManager, addServices, createSubmission, getArrayType, getArrayTypes, getCredentials, getDataFrame, getDataFrameList, getDefaultServices, getFolderName, getIdMap, getIdMapList, getProbesetList, getRoot, getServiceRoot, getServices, init, setCredentials, setOptions, setServices, addServices.ServiceManager, createSubmission.AnnotationNetAffx, getArrayType.Annotation, getArrayTypes.Annotation, getCredentials.Annotation, getDataFrame.Annotation, getDataFrameList.ServiceManager, getDefaultServices.ServiceManager, getFolderName.Annotation, getIdMap.Annotation, getIdMapList.ServiceManager, getProbesetList.AnnotationAffx, getRoot.Annotation, getServiceRoot.Annotation, getServices.ServiceManager, init.Annotation, setCredentials.Annotation, setCredentials.AnnotationAffx, setOptions.Annotation, setServices.ServiceManager Package: illuminaio Exports: readIDAT, readBPM, readBGX Package: imageHTS Exports: parseImageConf, segmentWells, extractFeatures, readLearnTS, predictCellLabels, summarizeWells, segmentATH, getCellFtrsATH, segmentYeastBF, segmentRing, installWebQuery, popWebQuery, installCellPicker, popCellPicker, makeCellHTS, fileHTS, readHTS, parseDCF, collectCellFeatures, getWellFeatures, getUnames, prw2uname, uname2prw, rowcol2well, well2rowcol, well2wellid, zprime, highlightSegmentation, countObjects, getImageConf ExportClasses: imageHTS Package: IMPCdata Exports: getPhenCenters, printPhenCenters, getPipelines, printPipelines, getParameters, printParameters, getProcedures, printProcedures, getGenes, printGenes, getAlleles, printAlleles, getStrains, printStrains, getName, getZygosities, getIMPCTable, getIMPCDataset Package: impute Exports: impute.knn Package: INPower Exports: INPower Package: inSilicoDb Exports: getDatasetList, getDatasetPlatformList, getPlatformList, getDatasetInfo, getPlatforms, getDataset, getDatasets, getDefaultCuration, getCurationInfo, getAnnotations, InSilicoLogin, InSilicoLogout, getInSilicoUserDetails Package: inSilicoMerging Exports: merge, plotMDS, plotRLE, plotGeneWiseBoxPlot Package: intansv Exports: methodsMerge, plotChromosome, plotRegion, readBreakDancer, readCnvnator, readDelly, readPindel, readSvseq, svAnnotation, geneAnnotation, readLumpy, readSoftSearch Package: interactiveDisplay Exports: display ExportMethods: altgr, simplenet, bicgo, gridtweak, gridsvgjs, display Package: interactiveDisplayBase Exports: display ExportMethods: display Package: inveRsion Exports: setUpGenoDatFile, setUpGenoDatSNPmat, codeHaplo, ROIGenoDat, manual, scanInv ExportMethods: accBic, getClassif, getInv, getROIs, initialize, listInv, plot, show ExportClasses: accuracy, GenoDat, GenoDatROI, HaploCode, inversion, inversionList, scan Package: iontree Exports: saveMSnRaw, getMetaInfo, hasMS2, buildIonTree, plotSpectrum, getMSnRaw, formatSpec, topIons, distMS2, createDB, metaDataImport, mzImport, searchMS2, rs2iontree ExportMethods: show, plot ExportClasses: iontree Package: iPAC Exports: ClusterFind, get.AASeq, get.AlignedPositions, get.Positions, get.SingleLetterCode, nmc, Plot.Protein.Linear, get.Remapped.Order Package: IPPD Exports: sweepline, analyzeLCMS, read.mzXML, new.mzXML ExportMethods: show, getPeaklist, fitModelParameters, threshold, visualize ExportClasses: peaklist, modelfit Package: IRanges Exports: as.data.frame.GappedRanges, as.data.frame.Hits, as.data.frame.RangedData, as.data.frame.Ranges, as.list.Vector, as.list.CompressedNormalIRangesList, as.list.Hits, duplicated.Dups, duplicated.CompressedList, head.Vector, sort.List, tail.Vector, unique.CompressedList, unique.CompressedRleList, unique.SimpleRleList, window.Vector, window.vector, window.factor, window.NULL, window.Rle, window<-.Vector, window<-.vector, window<-.factor, splitAsList, seqapply, mseqapply, tseqapply, seqsplit, seqby, multisplit, solveUserSEW0, IRanges, solveUserSEW, successiveIRanges, breakInChunks, whichAsIRanges, asNormalIRanges, rangeComparisonCodeToLetter, NCList, IntervalTree, IntervalForest, H2LGrouping, Dups, PartitioningByEnd, PartitioningByWidth, PartitioningMap, RangedData, RangedDataList, RangedSelection, FilterRules, FilterMatrix, RDApplyParams, RangesList, IRangesList, RleViewsList, CompressedHitsList, %over%, %within%, %outside%, MaskCollection.show_frame, Mask, read.gapMask, read.agpMask, read.liftMask, read.rmMask, read.trfMask, newViews, successiveViews, LogicalList, IntegerList, NumericList, ComplexList, CharacterList, RawList, RleList, DataFrameList, SplitDataFrameList, showAsCell, mstack, mid, isNormal, whichFirstNotNormal, subject, ranges, ranges<-, Views, trim, subviews, viewApply, viewMins, viewMaxs, viewSums, viewMeans, viewWhichMins, viewWhichMaxs, viewRangeMins, viewRangeMaxs, nobj, grouplength, members, vmembers, togroup, togrouplength, high2low, low2high, grouprank, togrouprank, mapOrder, findRange, splitRanges, relistToClass, splitAsListReturnedClass, extractList, columnMetadata, columnMetadata<-, universe, universe<-, space, ngap, nir_list, active, active<-, desc, desc<-, maskedwidth, maskedratio, collapse, score, score<-, rdapply, evalSeparately, subsetByFilter, params, rangedData, rangedData<-, applyFun, applyFun<-, applyParams, applyParams<-, filterRules, filterRules<-, simplify, simplify<-, reducerFun, reducerFun<-, reducerParams, reducerParams<-, iteratorFun, iteratorFun<-, map, pmap, mapCoords, pmapCoords, shift, narrow, resize, flank, reflect, promoters, restrict, threebands, reduce, gaps, disjoin, isDisjoint, disjointBins, reverse, coverage, slice, punion, pintersect, psetdiff, pgap, findOverlaps, countOverlaps, overlapsAny, subsetByOverlaps, mergeByOverlaps, precede, follow, nearest, distance, distanceToNearest, expand, tile ExportMethods: runsum, runmean, runwtsum, runq, showAsCell, mstack, mid, isNormal, whichFirstNotNormal, subject, ranges, ranges<-, Views, trim, subviews, viewApply, viewMins, viewMaxs, viewSums, viewMeans, viewWhichMins, viewWhichMaxs, viewRangeMins, viewRangeMaxs, nobj, grouplength, members, vmembers, togroup, togrouplength, high2low, low2high, grouprank, togrouprank, mapOrder, findRange, splitRanges, relistToClass, splitAsListReturnedClass, extractList, columnMetadata, columnMetadata<-, universe, universe<-, space, ngap, nir_list, active, active<-, desc, desc<-, maskedwidth, maskedratio, collapse, score, score<-, rdapply, evalSeparately, subsetByFilter, params, rangedData, rangedData<-, applyFun, applyFun<-, applyParams, applyParams<-, filterRules, filterRules<-, simplify, simplify<-, reducerFun, reducerFun<-, reducerParams, reducerParams<-, iteratorFun, iteratorFun<-, map, pmap, shift, narrow, resize, flank, reflect, promoters, restrict, threebands, reduce, gaps, disjoin, isDisjoint, disjointBins, reverse, coverage, slice, punion, pintersect, psetdiff, pgap, findOverlaps, countOverlaps, overlapsAny, subsetByOverlaps, precede, follow, nearest, distance, distanceToNearest, expand, tile, length, length<-, names, names<-, nrow, NROW, ncol, NCOL, dim, rownames, rownames<-, colnames, colnames<-, dimnames, dimnames<-, [, [<-, [[, [[<-, $<-, as.vector, as.integer, as.matrix, as.data.frame, as.list, as.table, coerce, c, show, ==, <=, match, duplicated, unique, anyDuplicated, %in%, order, sort, rank, xtfrm, is.unsorted, Ops, Math, Math2, Summary, Complex, summary, rev, rep, head, tail, drop, start, start<-, end, end<-, width, width<-, min, max, range, which.max, which.min, diff, mean, var, cov, cor, sd, median, quantile, mad, IQR, smoothEnds, runmed, subset, window, window<-, aggregate, transform, nchar, chartr, tolower, toupper, sub, gsub, unlist, stack, split<-, unsplit, relist, update, append, !, which, merge, split, with, within, t, is.na, by, cbind, rbind, eval, lapply, pmax, pmin, pmax.int, pmin.int, paste, rep.int, table, tapply, union, intersect, setdiff, updateObject, values, values<-, classNameForDisplay, queryHits, subjectHits, queryLength, subjectLength, compare, selfmatch, runLength, runValue<-, shiftApply, elementLengths, isEmpty, revElements, endoapply, mendoapply, as.env ExportClasses: functionORNULL, CompressedList, Ranges, RangesORmissing, IRanges, NormalIRanges, NCList, IntervalTree, IntervalForest, Grouping, ManyToOneGrouping, H2LGrouping, Dups, Partitioning, PartitioningByEnd, PartitioningByWidth, PartitioningMap, Views, RleViews, MaskCollection, AtomicList, CompressedAtomicList, SimpleAtomicList, LogicalList, CompressedLogicalList, SimpleLogicalList, IntegerList, CompressedIntegerList, SimpleIntegerList, NumericList, CompressedNumericList, SimpleNumericList, ComplexList, CompressedComplexList, SimpleComplexList, CharacterList, CompressedCharacterList, SimpleCharacterList, RawList, CompressedRawList, SimpleRawList, RleList, CompressedRleList, SimpleRleList, RangesList, SimpleRangesList, IRangesList, CompressedIRangesList, SimpleIRangesList, NormalIRangesList, CompressedNormalIRangesList, SimpleNormalIRangesList, GappedRanges, ViewsList, SimpleViewsList, RleViewsList, SimpleRleViewsList, DataFrameList, SimpleDataFrameList, SplitDataFrameList, CompressedSplitDataFrameList, SimpleSplitDataFrameList, RangedData, RangedDataList, FilterRules, FilterMatrix, RDApplyParams, HitsList, CompressedHitsList, RangedSelection, expressionORfunction Package: iSeq Exports: iSeq1, iSeq2, peakreg, mergetag, plotreg Package: isobar Exports: IBSpectraTypes ExportMethods: as.data.frame ExportClasses: IBSpectra, ProteinGroup Package: IsoGeneGUI Exports: IsoGeneGUI, IsoGeneGUIHelp Package: ITALICS Exports: ITALICS, analyseCGH, getQuartet, getResidu, getCorrection, getEffet, getConfDat, getModel, readQuartetCopyNb, getSnpInfo, fromSnpToQuartet, fromQuartetToSnp, addInfo, trainITALICS Package: iterativeBMA Exports: BssWssFast, bma.predict, brier.score, imageplot.iterate.bma, iterateBMAglm.train, iterateBMAglm.train.predict, iterateBMAglm.train.predict.test, iterateBMAglm.wrapper Package: iterativeBMAsurv Exports: assignRiskGroup, crossVal, crossVal.final.calc, crossVal.fold, crossVal.init, crossVal.run, crossVal.tabulate, imageplot.bma.mod, imageplot.iterate.bma.surv, iterateBMAinit, iterateBMAsurv.train, iterateBMAsurv.train.predict.assess, iterateBMAsurv.train.wrapper, predictBicSurv, predictiveAssessCategory, printTopGenes, singleGeneCoxph Package: jmosaics Exports: jmosaicsPattern, readBinsMultiple Package: joda Exports: differential.probs, regulation.scores, deregulation.scores, deregulation.p.values Package: KCsmart Exports: calcSpm, calcSpmCollection, getSigSegments, findSigLevelTrad, findSigLevelFdr, plotScaleSpace, idPoints, compareSpmCollection, getSigRegionsCompKC ExportMethods: plot, write.table, initialize, show, [[, [, [[<- ExportClasses: samplePointMatrix, sigSegments, spmCollection, compKc, compKcSigRegions Package: kebabs Exports: DNAVector, RNAVector, AAVector, genRandBioSeqs, annotationMetadata, annotationMetadata<-, annotationCharset, positionMetadata, positionMetadata<-, spectrumKernel, mismatchKernel, motifKernel, gappyPairKernel, linearKernel, symmetricPairKernel, getKernelMatrix, getExRep, getExRepQuadratic, getFeatureWeights, linWeight, expWeight, gaussWeight, swdWeight, getSVMSlotValue, seqKernelAsChar, evaluatePrediction, showAnnotatedSeq, kebabsDemo ExportMethods: kbsvm, predict, show, kernelParameters, as.KernelMatrix, getPredictionProfile, plot, profiles, baselines, sequences, featureWeights, featureWeights<-, modelOffset, modelOffset<-, cvResult, cvResult<-, modelSelResult, modelSelResult<-, svmModel, svmModel<-, probabilityModel, probabilityModel<-, gridRows, gridColumns, gridErrors, performance, selGridRow, selGridCol, fullModel, length, width, names, names<-, performCrossValidation, trainSVM, predictSVM, SVindex, getFeatureSpaceDimension ExportClasses: DNAVector, RNAVector, AAVector Package: KEGGgraph ExportMethods: getDisplayName, getEntryID, getKEGGID, getKEGGgeneLink, getType, getName, getSubtype, getValue, getTitle, getComponent, getPathwayInfo, getReactions, subtypeDisplay, getSubstrate, getProduct, show, nodes, edges, nodes<- ExportClasses: KEGGEdge, KEGGGroup, KEGGNode, KEGGPathwayInfo, KEGGReaction, KEGGEdgeSubType, KEGGGraphics, KEGGPathway Package: keggorthology Exports: getKOprobes, indRender, keggDF2graph, getKOtags Package: KEGGprofile Exports: col_by_value, convertId, download_KEGGfile, download_latest_pathway, find_enriched_pathway, newIdMatrix, parse_XMLfile, plot_pathway, plot_pathway_cor, plot_profile Package: KEGGREST Exports: keggInfo, keggList, listDatabases, keggFind, keggGet, keggConv, keggLink, mark.pathway.by.objects, color.pathway.by.objects Package: lapmix Exports: lapmix.Fit, laptopTable, lap.volcanoplot Package: LBE Exports: LBEa, LBEplot, LBE, LBEsummary, LBEwrite Package: les Exports: triangWeight, rectangWeight, gaussWeight, epWeight ExportMethods: plot, show, summary, threshold, regions, ci, export, estimate, chi2, Les ExportClasses: Les Package: limma ExportMethods: show ExportClasses: RGList, MAList, EListRaw, EList, MArrayLM, TestResults, LargeDataObject, Roast, MDS Package: LiquidAssociation ExportMethods: CNM.full, CNM.simple, getsGLA, getsLA, GLA, LA, plotGLA Package: lmdme ExportMethods: summary, show, screeplot, residuals, resid, print, permutation, p.values, p.adjust, modelDecomposition, model, loadingplot, lmdme, leverage, fitted.values, fitted, design, decomposition, componentsType, components, coefficients, coef, biplot, F.p.values ExportClasses: lmdme Package: LMGene Exports: genediff, glog, LMGene, lnorm, lnormeS, neweS, norm, psmeans, plotMeanSD, rowaov, tranest, tranestAffyProbeLevel, transeS, pvadjust Package: logicFS Exports: getMatEval, logic.bagging, logic.oob, logic.pimp, logicFS, make.snp.dummy, vim.chisq, vim.ebam, vim.logicFS, vim.norm, vim.signperm, vim.individual, vim.set, contr.none, contr.snps, mlogreg, vim.singleBoth, vim.singleRemove, vim.snp, vim.input, vim.set, vim.approxPval, vim.permInput, vim.permSNP, vim.permSet, getXy Package: logitT Exports: logitTAffy Package: lol Exports: lasso, matrixLasso, plotGW, lasso.cv, lasso.stability, lasso.simultaneous, lasso.multiSplit, lmMatrixFit, getLambdaNcoef, print.lol, print.lolMatrix ExportClasses: lol, lolMatrix Package: LPE Exports: resamp.adj, quartile.normalize, quan.norm, preprocess, permute, n.genes.adaptive.int, mt.rawp2adjp.LPE, lpe, lowess.normalize, iqr, am.trans, baseOlig.error, baseOlig.error.step1, baseOlig.error.step2, fdr.adjust, fixbounds.predict.smooth.spline Package: LPEadj Exports: adjBaseOlig.error, adjBaseOlig.error.step1, adjBaseOlig.error.step2, calculateLpeAdj, lpeAdj Package: lumi Exports: IlluminaID2nuID, addControlData2lumi, addNuID2lumi, addNuId2lumi, bgAdjust, detectOutlier, detectionCall, estimateLumiCV, getChipInfo, getControlData, getControlProbe, getControlType, getNuIDMappingInfo, id2seq, inverseVST, is.nuID, lumiB, lumiExpresso, lumiN, lumiQ, lumiR, lumiR.batch, lumiT, nuID2EntrezID, nuID2IlluminaID, nuID2RefSeqID, nuID2probeID, nuID2targetID, plotCDF, plotControlData, plotDensity, plotHousekeepingGene, plotSampleRelation, plotStringencyGene, plotVST, probeID2nuID, produceGEOPlatformFile, produceGEOSampleInfoTemplate, produceGEOSubmissionFile, rsn, seq2id, ssn, targetID2nuID, vst, rankinvariant, addAnnotationInfo, addControlData2methyLumiM, adjColorBias.quantile, adjColorBias.ssn, beta2m, bgAdjustMethylation, boxplotColorBias, colorBiasSummary, estimateBeta, estimateM, estimateIntensity, estimateMethylationBG, importMethyIDAT, lumiMethyB, lumiMethyC, lumiMethyN, lumiMethyR, m2beta, normalizeMethylation.quantile, normalizeMethylation.ssn, plotColorBias2D, plotColorBias1D, produceMethylationGEOSubmissionFile, smoothQuantileNormalization, lumiMethyStatus, gammaFitEM, methylationCall, plotGammaFit, getChrInfo ExportMethods: beadNum, beadNum<-, boxplot, combine, density, detection, detection<-, getHistory, hist, MAplot, pairs, plot, sampleNames<-, exprs, exprs<-, se.exprs, se.exprs<-, show, summary, [, coerce, controlData, controlData<-, asBigMatrix ExportClasses: LumiBatch Package: LVSmiRNA Exports: RLM, estVC, estVC.EList, estVC.RGList, lvs, lvs.EList, lvs.RGList, normalize.lvs, read.mir, summarize, summarize.EList, rlmFit, summarize.RGList, boxplot ExportMethods: plot, exprs, exprs<-, preproc, preproc<-, sampleNames, featureNames, probeNames Package: M3D Exports: M3D_Wrapper, plotMethProfile, pvals, readENCODEdata Package: macat Exports: buildMACAT, compute.sliding, loaddatapkg, discreteKernelize, discretize, discretize.tscores, discretizeAll, evalScoring, evaluateParameters, getResults, kernelize, kernelizeAll, kernelizeToPython, preprocessedLoader, scoring, plotSliding, kNN, rbf, basePairDistance, getsteps, kernelmatrix Package: maCorrPlot Exports: CIrho, CorrSample, CutCI, panel.corr.sample, plot.corr.sample, RandPairs Package: made4 Exports: array2ade4, bet.coinertia, between.graph, bga, bga.jackknife, bga.suppl, cia, commonMap, comparelists, do3d, getcol, graph1D, heatplot, html3D, ord, overview, plot.bga, plot.cia, plot.ord, plot.suppl, plotarrays, plotgenes, prettyDend, print.comparelists, randomiser, rotate3d, sumstats, suppl, topgenes, s.var, s.groups Package: maigesPack Exports: activeMod, activeModScoreHTML, activeNet, activeNetScoreHTML, addGeneGrps, addPaths, bootstrapCor, bootstrapMI, bootstrapT, calcA, calcW, classifyKNN, classifyKNNsc, classifyLDA, classifyLDAsc, classifySVM, classifySVMsc, compCorr, contrastsFitM, createMaigesRaw, createTDMS, deGenes2by2BootT, deGenes2by2Ttest, deGenes2by2Wilcox, deGenesANOVA, designANOVA, getLabels, heatmapsM, hierMde, hierM, kmeansMde, kmeansM, loadData, MI, normLoc, normOLIN, normRepLoess, normScaleLimma, normScaleMarray, plotGenePair, relNet2TGF, relNetworkB, relNetworkM, robustCorr, selSpots, somMde, somM, summarizeReplicates, tableClass, tablesDE ExportMethods: coerce, show, [ ExportClasses: maigesPreRaw, maigesRaw, maiges, maigesANOVA, maigesDE, maigesDEcluster, maigesClass, maigesRelNetM, maigesRelNetB, maigesActMod, maigesActNet Package: MAIT Exports: Biotransformations, classes, classifRatioClasses, classNum, featureID, featureInfo, featureSigID, identifyMetabolites, LSDResults, metaboliteTable, models, model, scores, MAITbuilder, method, pcaScores, plsScores, pcaLoadings, plsLoadings, loadings, getScoresTable, ovClassifRatioData, ovClassifRatioTable, parameters, peakAggregation, peakAnnotation, plotBoxplot, plotHeatmap, pcaModel, plsModel, plotPLS, plotPCA, pvalues, pvaluesCorrection, rawData, resultsPath, sampleProcessing, sigPeaksTable, spectralSigFeatures, Validation, MAITbuilder ExportMethods: summary, model, scores, loadings ExportClasses: MAIT, MAIT.Parameters, MAIT.FeatureData, MAIT.FeatureInfo, MAIT.PhenoData, MAIT.RawData, MAIT.Validation Package: makecdfenv Exports: getInfoInFile, make.cdf.env, make.cdf.package, pmormm, read.cdffile ExportMethods: name.levels<-, name.levels, pbase.levels<-, pbase.levels, pbase<-, pbase, show, tbase.levels<-, tbase.levels, tbase<-, tbase ExportClasses: Cdf Package: MantelCorr Exports: ClusterGeneList, ClusterList, DistMatrices, GetClusters, MantelCorrs, PermutationTest Package: maPredictDSC Exports: predictDSC, aggregateDSC, perfDSC Package: marray Exports: controlCode, mapGeneInfo, widget.mapGeneInfo, htmlPage, opVersionID, table2html, rbind.marrayInfo, cbind.marrayRaw, cbind.marrayNorm, maNum2Logic, maGeneTable, maCompPlate, maInd2Coord, maCoord2Ind, maCompCoord, maCompInd, maCompLayout, maGenControls, maDotsMatch, maPlate<-, maControls<-, read.marrayLayout, read.marrayInfo, read.marrayRaw, read.Spot, read.GenePix, read.Agilent, read.Galfile, read.SMD, checkTargetInfo, maNormMain, maNorm, maNormScale, maMed, maNormMed, maLoess, maNormLoess, ma2D, maNorm2D, maMAD, maNormMAD, maCompNormEq, maCompNormA, write.marray, write.xls, write.list, plot.marrayRaw, plot.marrayNorm, maDotsDefaults, maDefaultPar, maBoxplot, maPlot.func, maText, maLowessLines, maLoessLines, maLegendLines, maPlot, maImage.func, maImage, maPalette, maColorBar, maTop, maSelectGnames, stat.confband.text, stat.gnames, findID, mean.na, var.na, cor.na, length.na, log.na, quantile.na, order.na, scale.na, prod.na, rm.na, widget.marrayLayout, widget.marrayInfo, widget.marrayRaw, widget.TwoSamples, maTwoSamples, sum.na, URLstring, maInfo, addLines, addText, addPoints, URLstring, read.fname ExportMethods: maLabels, maLabels<-, maInfo<-, maInfo, maNgc<-, maNsr<-, maNsc<-, maNspots<-, maPlate<-, maControls<-, maLayout<-, maGnames<-, maTargets<-, maW<-, maGf<-, maRf<-, maGb<-, maRb<-, maA<-, maM<-, maMloc<-, maMscale<-, maNotes<-, coerce, maNspots, maNgr<-, maNgc, maNsr, maNsc, maSub, maPlate, maNotes, maGridRow, maGridCol, maSpotRow, maSpotCol, maPrintTip, maRf, maGf, maRb, maGb, maW, maLR, maLG, maM, maA, maLayout, maNgr, maControls, maNsamples, maGnames, maTargets, maMloc, maMscale, maNormCall, boxplot, image, points, text, lines, summary, show, [ ExportClasses: marrayInfo, marrayLayout, marrayRaw, marrayNorm, ShowLargeObject Package: maSigPro Exports: average.rows, get.siggenes, i.rank, make.design.matrix, maSigPro, maSigProUsersGuide, p.vector, PlotGroups, PlotProfiles, position, reg.coeffs, see.genes, stepback, stepfor, suma2Venn, T.fit, two.ways.stepback, two.ways.stepfor Package: MassArray Exports: ampliconPrediction, analyzeCpGs, bisConvert, expandSequence, calcMW, calcPercentAdduct, calcPercentConversion, calcMeth, convControl, countCGs, createWiggle, estimatePrimerDimer, evaluateSNPs, findCollisions, findPeaks, findFragments, identifySNPs, inSilicoFragmentation, importEpiTyperData, importEpiTyperData.new, isAssayable, numCollisions, plot.MassArrayData, rnaDigest, sum.MassArraySpectrum ExportMethods: combine, position, position<-, revComplement, samples, samples<- ExportClasses: MassArrayPeak, MassArraySpectrum, MassArrayFragment, MassArrayData Package: MassSpecWavelet Exports: cwt, getLocalMaximumCWT, getRidge, getRidgeLength, identifyMajorPeaks, localMaximum, peakDetectionCWT, plotLocalMax, plotPeak, plotRidgeList, tuneInPeakInfo Package: matchBox Exports: calcHypPI, computeCat, plotCat, filterRedundant, mergeData Package: MBASED Exports: runMBASED Package: MBCB Exports: mbcb.parseFile, mbcb.correct, mbcb.main, bg.rma, bg.mcmc, mbcb.gui Package: mBPCR Exports: logAdd, indexLA0, estGlobParam, computeLA0Vect, computeA10, computeRecursions, computeRegrCurve, computePCReg, computeMBPCR, writeEstProfile, importCNData, estProfileWithMBPCR, estProfileWithMBPCRforOligoSnpSet, plotEstProfile Package: mcaGUI Exports: mcaGUI, pmg.gw, pmg.add, pmg.addMenubar, pmg.eval, pmgRepeatTrials, plotecdf, kurtosis, cluster, richness, diversityfun, principle_component, bootstrap, skewness Package: MCRestimate Exports: class.factor.format, ClassifierBuild, ClassifierBuild.default, identity, varSel.highest.t.stat, varSel.highest.var, varSel.AUC, cluster.kmeans.mean, varSel.removeManyNA, varSel.impute.NA, important.variable.names, MCRindError, plotIndGroupVotes, intersectList, MCRwrongsamples, MCRconfusion, MCRestimateMerge, MCRestimate, MCRestimate.default, plot.MCRestimate, PLR, predict.PLR, replace.NA, select.NA.elements, SVM.OVA.wrap, RF.wrap, PAM.wrap, PLR.wrap, SVM.wrap, GPLS.wrap Package: mdqc Exports: mdqc, prcomp.robust Package: MeasurementError.cor Exports: cor.me.vector, cor.me.matrix Package: MEDIPS ExportMethods: sample_name, genome_name, number_regions, chr_names, chr_lengths, genome_count, extend, show, window_size, shifted, uniq ExportClasses: MEDIPSset, COUPLINGset Package: MEDME ExportMethods: initialize, chr, pos, logR, smoothed, AMS, RMS, CG, org, [, show ExportClasses: MEDMEset Package: MEIGOR Exports: CeSSR, CeVNSR, essR_multistart, MEIGO, rvnds_hamming, essR, runBayesFit, cur_params Package: MergeMaid Exports: mergeExprs ExportMethods: exprs, geneNames, names, notes, phenoData, length, show, summary, geneStudy, coeff, stdcoeff, zscore, pairwise.cors, maxcors, integrative.cors, modelOutcome, intCor, plot, hist, intcorDens, intersection, exprs<-, geneNames<-, names<-, notes<-, phenoData<-, geneStudy<-, coeff<-, stdcoeff<-, zscore<- ExportClasses: mergeExpressionSet, mergeCor, mergeCoeff Package: MeSHDbi Exports: makeGeneMeSHPackage, MeSHDb ExportMethods: columns, keytypes, keys, select, dbconn, dbfile, dbschema, dbInfo, species, packageName, nomenclature, listDatabases, meshVersion ExportClasses: MeSHDb Package: meshr ExportMethods: meshHyperGTest, meshIds, meshCategory, meshAnnotation, meshDatabase, show, summary, save.pdf, initialize, geneIds, universeGeneIds, universeGeneIds<-, annotation, annotation<-, category, category<-, database, database<-, pvalueCutoff, pvalueCutoff<-, pAdjust, pAdjust<-, makeValidParams ExportClasses: MeSHHyperGParams, MeSHHyperGResult Package: messina Exports: messina, messinaDE, messinaSurv, messinaTopResults ExportMethods: show, plot ExportClasses: MessinaSurvResult, MessinaClassResult Package: metaArray Exports: poe.mcmc, poe.em, intcor Package: Metab Exports: MetReport, normalizeByInternalStandard, normalizeByBiomass, removeFalsePositives, buildLib, htest, MetReportNames Package: metabomxtr ExportMethods: xdesign, zdesign, yvals Package: metagene Exports: parseFeatures, parseRegions, plotMatrices Package: metagenomeSeq Exports: aggregateByTaxonomy, aggTax, biom2MRexperiment, calculateEffectiveSamples, calcNormFactors, correlationTest, correctIndices, cumNorm, cumNormMat, cumNormStat, cumNormStatFast, expSummary, exportMat, exportStats, fitDO, fitMeta, fitPA, fitSSTimeSeries, fitTimeSeries, fitZig, filterData, load_biom, load_meta, load_metaQ, load_phenoData, makeLabels, MRcoefs, MRcounts, MRfulltable, MRtable, MRexperiment2biom, plotBubble, plotCorr, plotGenus, plotMRheatmap, plotOTU, plotOrd, plotRare, plotFeature, plotTimeSeries, plotClassTimeSeries, uniqueFeatures, ssFit, ssIntervalCandidate, ssPerm, ssPermAnalysis, trapz, zigControl, newMRexperiment, posterior.probs, normFactors, libSize ExportMethods: [, colSums, rowSums, colMeans, rowMeans ExportClasses: MRexperiment Package: metahdep Exports: metahdep.FEMA, metahdep.format, metahdep.HBLM, metahdep, metahdep.REMA, getPLM.es, metahdep.list2dataframe, LinMod.MetAn.dep.REMA, LinMod.REMA.dep, LinMod.REMA.delta.split, LinMod.HBLM.fast.dep, new.LinMod.HBLM.fast.dep.delta.split, LinMod.MetAn.dep.FEMA, metahdep.check.X, get.M, tr, id, center.columns, mod, get.varsigma.v Package: metaMS Exports: runGC, runLC, peakDetection, matchExpSpec, write.msp, construct.msp, filter.msp, read.msp, to.msp, addRI, treat.DB, matchSamples2DB, matchSamples2Samples, constructExpPseudoSpectra, getFeatureInfo, getAnnotationMat, AnnotateFeature, AnnotateTable, plotPseudoSpectrum, processStandards, alignmentLC, runCAMERA, getAnnotationLC, getPeakTable, createSTDdbGC, createSTDdbLC, readStdInfo, generateStdDBGC, generateStdDBLC, metaMSsettings, metaSetting ExportMethods: metaSetting, metaSetting<-, show ExportClasses: metaMSsettings Package: metaSeq Exports: meta.readData, meta.oneside.noiseq, Fisher.test, Stouffer.test, other.oneside.pvalues, Accelerate.NOISeq, Reset.Accelerate.NOISeq Package: metaseqR Exports: as.class.vector, calc.otr, calc.f1score, check.contrast.format, check.file.args, check.libsize, check.num.args, check.packages, check.parallel, check.text.args, combine.bonferroni, combine.maxp, combine.minp, combine.simes, combine.weight, construct.gene.model, diagplot.avg.ftd, diagplot.boxplot, diagplot.cor, diagplot.de.heatmap, diagplot.edaseq, diagplot.filtered, diagplot.ftd, diagplot.mds, diagplot.metaseqr, diagplot.noiseq, diagplot.pairs, diagplot.roc, diagplot.venn, diagplot.volcano, disp, downsample.counts, estimate.aufc.weights, estimate.sim.params, filter.exons, filter.genes, filter.high, filter.low, get.annotation, get.biotypes, get.dataset, get.defaults, get.ensembl.annotation, get.exon.attributes, get.gc.content, get.gene.attributes, get.host, get.preset.opts, get.ucsc.annotation, get.ucsc.credentials, get.ucsc.dbl, get.ucsc.tabledef, get.ucsc.query, get.valid.chrs, get.weights, load.bs.genome, make.contrast.list, make.fold.change, make.grid, make.html.body, make.html.cells, make.html.header, make.html.rows, make.html.table, make.matrix, make.permutation, make.sample.list, make.sim.data.tcc, make.sim.data.sd, make.stat, make.transformation, make.venn.areas, make.venn.colorscheme, make.venn.counts, make.venn.pairs, metaseqr, normalize.deseq, normalize.edaseq, normalize.edger, normalize.nbpseq, normalize.noiseq, read2count, read.targets, reduce.exons, reduce.gene.data, stat.bayseq, stat.deseq, stat.edger, stat.limma, stat.nbpseq, stat.noiseq, validate.alg.args, validate.list.args, wapply Package: methVisual Exports: plotAbsMethyl, MethLollipops, heatMapMeth, matrixSNP, plotMatrixSNP, methCA, methFisherTest, methWhitneyUTest, cgInAlign, findNonAligned, Cooccurrence, MethAlignNW, cgMethFinder, makeDataMethGFF, MethDataInput, selectRefSeq, readBisulfFASTA, makeLocalExpDir, makeTabFilePath, MethylQC, coversionGenom Package: methyAnalysis Exports: MethyGenoSet, annotateDMRInfo, annotateGRanges, detectDMR.slideWin, export.methyGenoSet, getContinuousRegion, identifySigDMR, export.DMRInfo, MethyLumiM2GenoSet, smoothMethyData, createTranscriptTrack, buildAnnotationTracks, heatmapByChromosome, plotHeatmapByGene, plotMethylationHeatmapByGene, plotTracksWithDataTrackInfo, checkChrName, estimateCMR.methylation ExportMethods: asBigMatrix, exprs, exprs<-, methylated, unmethylated, detection, methylated<-, unmethylated<-, detection<-, getHistory, combine, [, coerce, locData, locData<-, chrNames ExportClasses: MethyGenoSet Package: MethylAid Exports: summarize ExportMethods: visualize, show ExportClasses: summarizedData Package: MethylMix Exports: MethylMix, MethylMix_PlotModel Package: methylPipe ExportMethods: [[, [[<-, [, $, show, chr, binC, binmC, binrC, nbins, binscore, binscore<-, mCsmoothing, findDMR, methstats ExportClasses: GEcollection, GElist, BSdata, BSdataSet Package: MethylSeekR Exports: readMethylome, readSNPTable, removeSNPs, plotAlphaDistributionOneChr, segmentPMDs, plotPMDSegmentation, savePMDSegments, calculateFDRs, segmentUMRsLMRs, plotFinalSegmentation, saveUMRLMRSegments Package: methylumi Exports: methylumiR, extractBarcodeAndPosition, normalizeMethyLumiSet, getAssayDataNameSubstitutions, estimateM, methylumIDAT, lumIDAT, methylumiCSV, lumiCSV, methylumi.diagnostics, qc.probe.plot, cy3, cy5, getBarcodes, stripBeadNs, stripBeadSDs, stripMethyLumiSet, psummary, negctls.stderr, methylumi.bgcorr, IDATtoDF, IDATsToDFs, readMethyLumIDAT, designItoMandU, designIItoMandU, mergeProbeDesigns, NChannelSetToMethyLumiSet, subset450kas27k, subset27kas450k, subsetCommonProbes, stripOOB, plotNegOob, compare.chips, .mclapply ExportMethods: getHistory, betas, pvals, exprs, summary, show, combine, hist, pairs, [, QCdata, plotSampleIntensities, qcplot, total.intensity, methylated, unmethylated, unmethylated<-, methylated<-, QCdata<-, exprs<-, diagnostics, Cy3.N, Cy5.N, pvals<-, betas<-, controlTypes, corplot, negctls.stderr, controlData, controlData<-, detection, detection<-, unmethylated.N, unmethylated.N<-, pval.detect<-, pval.detect, sampleNAs, probeNAs, plotNAs, normctls, negctls, methylated.N, methylated.N<-, featureFilter, varFilter, intensities.OOB, intensities.IB, negnorm, Cy3<-, Cy5<-, intensities.OOB.allelic, intensitiesByChannel, intensities.M, intensities.U, combine27k450k, dataType, dataType<- ExportClasses: MethyLumiSet, MethyLumiQC, MethyLumi, MethyLumiM, methylData Package: Mfuzz Exports: acore, cselection, Dmin, fill.NA, filter.NA, filter.std, filter.std, kmeans2, kmeans2.plot, mestimate, membership, mfuzz, mfuzz.plot, mfuzz.plot2, Mfuzzgui, mfuzzColorBar, overlap, overlap.plot, partcoef, randomise, standardise, standardise2, top.count, table2eset Package: MGFM Exports: getMarkerGenes, getHtmlpage Package: mgsa Exports: readGAF ExportMethods: mgsa, subMgsaSets, itemIndices, length, setAnnotations, itemAnnotations, plot, show, setsMcmcPost, pMcmcPost, betaMcmcPost, alphaMcmcPost, restarts, steps, setsResults, pPost, betaPost, alphaPost, studySetSizeInPopulation, populationSize ExportClasses: MgsaSets, MgsaMcmcResults, MgsaResults, MgsaGoSets Package: MiChip Exports: parseRawData, outputAnnotatedDataMatrix, returnAnnotatedDataMatrix, removeUnwantedRows, standardRemoveRows, myForgivingMedian, setIntensityCutoff, correctForFlags, summarizeIntensitiesAsMedian, normalizePerChipMedian, boxplotData, boxplotDataNoFile, plotIntensitiesScatter, workedExampleMedianNormalize, workedExampleNotNormalizedData Package: microRNA Exports: get_selfhyb_subseq, show_selfhyb_counts, show_selfhyb_lengths, seedRegions, matchSeeds, RNA2DNA Package: MIMOSA Exports: ConstructMIMOSAExpressionSet, MIMOSA, MIMOSAExpressionSet, asinh_trans, boxplotMIMOSAResultList, combine.MIMOSA, countsTable, fdr, getW, getZ, volcanoPlot Package: MineICA Exports: annot2Color, annotFeatures, annotFeaturesComp, annotFeaturesWithBiomaRt, annotInGene, annotReciprocal, buildIcaSet, buildMineICAParams, clusterFastICARuns, clusterSamplesByComp, clusterSamplesByComp_multiple, clusVarAnalysis, compareAn, compareAn2graphfile, compareGenes, cor2An, getProj, getSdExpr, hypergeoAn, nbOccInComp, nodeAttrs, plotAllMix, plotCorGraph, plot_heatmapsOnSel, plotMix, plotPosAnnotInComp, plotPosSamplesInComp, qualVarAnalysis, quantVarAnalysis, relativePath, runAn, runCompareIcaSets, runEnrich, runICA, selectContrib, selectFeatures_IQR, selectWitnessGenes, writeGenes, writeHtmlResTestsByAnnot, writeProjByComp, writeRnkFiles ExportMethods: dat, dat<-, datByGene, datByGene<-, nbComp, organism, organism<-, A, Alist, A<-, S, S<-, SByGene, SByGene<-, [, [<-, getComp, indComp, indComp<-, compNames, compNames<-, witGenes<-, witGenes, Slist, SlistByGene, chipVersion, chipVersion<-, chipManu<-, chipManu, refSamples<-, refSamples, typeID<-, typeID, annotfile, annotfile<-, Afile, Afile<-, Sfile, Sfile<-, datfile, datfile<-, resPath, resPath<-, genesPath, genesPath<-, annot2col, annot2col<-, selCutoff, selCutoff<-, pvalCutoff, pvalCutoff<-, geneNames, mart, mart<- ExportClasses: IcaSet, MineICAParams Package: minet Exports: aracne, build.mim, clr, fscores, minet, mrnet, mrnetb, pr, rates, show.pr, show.roc, auc.pr, auc.roc, validate Package: minfi Exports: getManifest, getProbeInfo, getManifestInfo, IlluminaMethylationManifest, IlluminaMethylationAnnotation, getControlAddress, getControlTypes, getRed, getGreen, getMeth, getUnmeth, getBeta, getM, getCN, getMethSignal, getOOB, getSnpBeta, dropMethylationLoci, getLocations, getAnnotation, getAnnotationObject, mapToGenome, getIslandStatus, getProbeType, getSnpInfo, addSnpInfo, dropLociWithSnps, normalize.illumina.control, bgcorrect.illumina, preprocessRaw, preprocessIllumina, preprocessSWAN, preprocessQuantile, preprocessFunnorm, preprocessNoob, RGChannelSet, RGChannelSetExtended, MethylSet, RatioSet, GenomicMethylSet, GenomicRatioSet, read.450k, read.450k.sheet, read.450k.exp, logit2, ilogit2, dmpFinder, mdsPlot, plotCpg, plotBetasByType, detectionP, qcReport, controlStripPlot, densityBeanPlot, densityPlot, getQC, plotQC, addQC, minfiQC, fixMethOutliers, getSex, plotSex, addSex, bumphunter, blockFinder, cpgCollapse, estimateCellCounts ExportMethods: show, initialize, getBeta, getM, getCN, getMeth, getUnmeth, getManifest, annotation, preprocessMethod, sampleNames, featureNames, pData, mapToGenome, ratioConvert, bumphunter ExportClasses: RGChannelSet, RGChannelSetExtended, MethylSet, RatioSet, GenomicMethylSet, GenomicRatioSet, IlluminaMethylationManifest, IlluminaMethylationAnnotation Package: MinimumDistance Exports: mindist<-, nMAD<-, offspringNames<-, pedigree<-, DNAcopyParam, FilterParamMD, MAP, MAP2, MDRanges, MinDistExperiment, MinDistGRanges, MinDistParam, ParentOffspring, ParentOffspringList, Pedigree, PennParam, TrioSet, TrioSetList, TrioSetListLD, acf2, calculateMindist, denovo, denovoDuplication, denovoHemizygous, denovoHomozygous, father, filterExperiment, mad2, mdLegend, mindist, mother, nMAD, offspring, offspringNames, pedigree, pedigreeGrid, pedigreeName, pedigreeViewports, plotDenovo, segment2, trios ExportMethods: stack, show, reduce ExportClasses: TrioSetList, TrioSet, Pedigree, ParentOffspringList, ParentOffspring, MinDistPosterior, MinDistParam, MinDistGRanges, MinDistExperiment, MDRanges, FilterParamMD Package: MiPP Exports: cv.mipp.rule, get.mipp, get.mipp.lda, get.mipp.logistic, get.mipp.qda, get.mipp.svm.linear, get.mipp.svm.rbf, linearkernel.decision.function, mipp, mipp.preproc, mipp.rule, mipp.seq, pre.select, quant.normal, quant.normal2, rbfkernel.decision.function Package: MiRaGE Exports: MiRaGE, HS_conv_id, MM_conv_id, id_conv_gen, TBL2_HS_gen, TBL2_MM_gen, getMiRaGEData Package: miRNApath ExportMethods: show ExportClasses: mirnapath Package: miRNAtap Exports: getPredictedTargets, getTargetsFromSource, translate ExportMethods: select, keytypes, keys, columns ExportClasses: MirnaDb Package: Mirsynergy Exports: mirsynergy, print_modules2, plot_modules, summary_modules, plot_module_summary, tabular_module Package: missMethyl Exports: SWAN, densityByProbeType, varFit, topVar, getLeveneResiduals, SWAN.MethyLumiSet, SWAN.RGChannelSet, SWAN.default, varFit.MethylSet, varFit.DGEList, varFit.default, contrasts.varFit Package: mitoODE Exports: plotfit, plotk, getp0, fitmodel, loadFittedData, figure1, figure2, figure3a, figure3b, figure4 Package: MLInterfaces Exports: randomForestI, knnI, dldaI, nnetI, rpartI, ldaI, svmI, ldaI.predParms, qdaI, glmI.logistic, RABI, lvqI, naiveBayesI, baggingI, knn2, dlda2, rab, lvq, RAB, DAB, plsda2, svm2, ksvm2, xvalSpec, getVarImp, balKfold.xvspec, rdacvI, rdacvML, rdaI, rdaML, plotXvalRDA, makeLearnerSchema, standardMLIConverter, sldaI, fs.absT, fs.probT, ksvmI, knn.cvI, knn.cv2, adaI, fs.topVariance, hclustI, kmeansI, pamI, blackboostI, gbm2, BgbmI, plsdaI, confuTab ExportMethods: plot, show, RObject, confuMat, trainInd, precision, recall, sensitivity, macroF1, F1, acc, tp, tn, fp, fn, specificity, MLearn, planarPlot, Predict, getVarImp, trainScores, trainPredictions, testScores, testPredictions, predictions, predScores, predScore, fsHistory, report, getDist, getConverter ExportClasses: varImpStruct, classifierOutput, learnerSchema, xvalSpec, clusteringOutput Package: MLP Exports: addGeneSetDescription, getGeneSets, MLP, mlpBarplot, plotGeneSetSignificance, plotGOgraph Package: MLSeq Exports: classify, predictClassify ExportMethods: ref, trained, confusionMat, normalization, deseqTransform, method ExportClasses: MLSeq Package: MMDiff Exports: getPeakProfiles, findOutliers, getNormFactors, compHistDists, detPeakPvals, plotHistDists, plotPeak Package: mmnet Exports: topologicalAnalyzeNet, checkMgrastMetagenome, listMgrastProject, differentialAnalyzeNet, constructMetabolicNetwork, delMgrastInbox, estimateAbundance, generateMgrastWebkey, generateMgrastWebsession, getKOPathwayInfo, getMgrastAnnotation, listMgrastInbox, loadMetabolicData, loginMgrast, preprocessKOMetabolites, saveMetabolicData, submitMgrastJob, updateKEGGPathway, uploadMgrast, constructSSN, showMetagenomicNet Package: MmPalateMiRNA Exports: imputeKNN, fixOutliers, fixMVs, clustPlot ExportMethods: densityplot, levelplot, checkOutliers, checkMVs, filterArray, MADvsMedianPlot, MAplot Package: monocle Exports: newCellDataSet, detectGenes, reduceDimension, reducedDimS, reducedDimS<-, reducedDimW, reducedDimW<-, reducedDimA, reducedDimA<-, minSpanningTree, minSpanningTree<-, cellPairwiseDistances, cellPairwiseDistances<-, setOrderingFilter, orderCells, plot_spanning_tree, plot_genes_in_pseudotime, plot_genes_jitter, plot_genes_positive_cells, plot_clusters, differentialGeneTest, fitModel, compareModels, responseMatrix, clusterGenes, selectNegentropyGenes ExportClasses: CellDataSet Package: mosaics Exports: constructBins, readBins, mosaicsFit, mosaicsPeak, mosaicsRunAll, generateWig, mosaicsFitHMM, mosaicsPeakHMM, show, print, plot, estimates, export Package: MotifDb Exports: MotifDb ExportMethods: subset, export, show, query ExportClasses: MotifList Package: motifRG Exports: findMotif, findMotifFasta, findMotifFgBg, summaryMotif, plotMotif, motifLatexTable, motifHtmlTable, refinePWMMotif, refinePWMMotifExtend, getSequence Package: motifStack Exports: plotMotifLogo, plotMotifLogoA, plotXaxis, plotYaxis, colorset, motifStack, plotMotifLogoStack, plotMotifLogoStackWithTree, DNAmotifAlignment, plotMotifStackWithPhylog, plotMotifStackWithRadialPhylog, motifSignature, motifCloud, readPCM ExportMethods: plot, getIC, matrixReverseComplement, addBlank, pcm2pfm, signatures, frequence, nodelist, sigColor, trimMotif ExportClasses: pfm, pcm, ouNode, motifSig Package: MotIV Exports: motifMatch, generateDBScores, readDBScores, writeDBScores, getGademPWM, readGademPWMFile, readPWMfile, viewAlignments, summary, plot, split, filter, makePWM, setFilter, combineMotifs, trimPWMedge, exportAsRangedData, similarity, viewMotifs, occurences, cooccurences, getPWM, nMotifs, motifDistances, motifHclust, motifCutree ExportMethods: show, summary, as.data.frame, combineMotifs, filter, split, exportAsTransfacFile, getPWM ExportClasses: motiv, matches, alignments, transcriptionFactor, filter Package: MPFE Exports: estimatePatterns, plotPatterns Package: mQTL.NMR Exports: align_mQTL, format_mQTL, format_mGWA, post_mQTL, pre_mQTL, process_mQTL, process_mGWA, summary_mQTL, alignSp, attachSegments, matchSegments, normalise, peakPeaks, ppersp, pplot, segmentateSp, selectRefSp, sgolay, sgolayDeriv, SRV, normalise_mQTL, simple.plot, SRV.plot, Top_SRV.plot, SRV_lod.plot, load_demo_data, load_datafiles, setupRSPA, configureRSPA, circle_mQTL Package: MSGFgui Exports: MSGFgui, currentData Package: MSGFplus Exports: chargeRange<-, db<-, enzyme<-, fragmentation<-, instrument<-, isotopeError<-, lengthRange<-, matches<-, mods<-, nMod<-, ntt<-, protocol<-, tda<-, tolerance<-, toleranceRange<-, toleranceUnit<-, chargeRange, db, enzyme, finished, fragmentation, getMSGFpar, import, instrument, isotopeError, lengthRange, matches, mods, msgfPar, msgfParChargeRange, msgfParEnzyme, msgfParFragmentation, msgfParFromID, msgfParGUI, msgfParInstrument, msgfParIsotopeError, msgfParLengthRange, msgfParMatches, msgfParModification, msgfParModificationList, msgfParNtt, msgfParProtocol, msgfParTda, msgfParTolerance, nMod, ntt, protocol, runMSGF, running, tda, tolerance, toleranceRange, toleranceUnit ExportClasses: msgfPar Package: msmsEDA Exports: pp.msms.data, gene.table, count.stats, counts.pca, counts.hc, norm.counts, counts.heatmap, disp.estimates, filter.flags, spc.barplots, spc.boxplots, spc.densityplots, spc.scatterplot, batch.neutralize Package: msmsTests Exports: msms.glm.pois, msms.glm.qlll, msms.edgeR, test.results, pval.by.fc, res.volcanoplot Package: MSnbase Exports: MSnSet, readMzXMLData, readMgfData, readMSData, readMSnSet, readMSnSet2, getEcols, grepEcols, readIspyData, writeMzTabData, readMzTabData, makeMTD, makePEP, makePRT, formatRt, fillUp, extractPrecSpectra, as.data.frame.Spectrum, as.data.frame.MSnSet, ms2df, as.ExpressionSet.MSnSet, as.MIAME.MIAPE, is.na.MSnSet, droplevels.MSnSet, combineFeatures, nQuants, featureCV, getRatios, makeImpuritiesMatrix, precSelection, precSelectionTable, t.MSnSet, updateFvarLabels, updateFeatureNames, updateSampleNames, normalise, get.amino.acids, get.atomic.mass, listOf, npcv, averageMSnSet, MSmap ExportMethods: coerce, show, [, [[, fileNames, msInfo, expemail, exptitle, ionSource, ionSourceDetails, analyser, analyzer, analyserDetails, analyzerDetails, detectorType, instrumentModel, instrumentManufacturer, instrumentCustomisations, qual, length, image, plot, plot2d, plotDensity, plotMzDelta, plotNA, MAplot, spectra, processingData, peaksCount, isEmpty, bin, calculateFragments, clean, compareSpectra, pickPeaks, removePeaks, removeReporters, smooth, addIdentificationData, removeNoId, removeMultipleAssignment, idSummary, intensity, mz, tic, ionCount, fromFile, centroided, centroided<-, precursorMz, precursorIntensity, precursorCharge, precScanNum, acquisitionNum, scanIndex, rtime, msLevel, collisionEnergy, polarity, trimMz, quantify, purityCorrect, header, dim, multiplex, multiLabels, width, reporterColours, reporterColors, reporterNames, reporterNames<-, writeMgfData, write.exprs, combine, experimentData<-, normalize, scale, log, exprsToRatios, impute, topN, filterNA, chromatogram, xic, FeaturesOfInterest, foi, description, FoICollection, addFeaturesOfInterest, rmFeaturesOfInterest, fnamesIn, compfnames, common, unique1, unique2, names, mzRes, plot3D, msMap, fileName, t ExportClasses: pSet, MIAPE, MSnExp, MSnProcess, MSnSet, Spectrum, Spectrum1, Spectrum2, ReporterIons, FeaturesOfInterest, FoICollection, FeatComp, MSmap Package: MSnID Exports: MSnID, MSnIDFilter ExportMethods: psms, psms<-, dim, show, names, update, length, as.numeric, $, $<-, [[, [[<-, proteins, accessions, peptides, recalibrate, mass_measurement_error, correct_peak_selection, optimize_filter, id_quality, evaluate_filter, apply_filter, assess_missed_cleavages, assess_termini, read_mzIDs Package: Mulcom Exports: mulCalc, mulDiff, mulFSG, mulOptPars, mulOptPlot, mulOpt, mulPerm, mulScores, mulCAND, mulDELTA, mulParOpt, mulInt, mulIndex ExportClasses: MULCOM, MULCOM_P Package: MultiMed Exports: medTest Package: multiscan Exports: multiscan Package: multtest Exports: MTP, EBMTP, as.list, mt.maxT, mt.minP, mt.plot, mt.rawp2adjp, mt.reject, mt.sample.label, mt.sample.rawp, mt.sample.teststat, mt.teststat, mt.teststat.num.denum, meanX, diffmeanX, FX, blockFX, twowayFX, lmX, lmY, coxY, get.Tn, boot.null, boot.resample, center.only, center.scale, quant.trans, fwer2gfwer, fwer2tppfp, fwer2fdr, get.index, ss.maxT, ss.minP, sd.maxT, sd.minP, wapply, corr.Tn, corr.null, IC.Cor.NA, IC.CorXW.NA, insert.NA, diffs.1.N, marg.samp, tQuantTrans, G.VS, ABH.h0, dens.est, Hsets, VScount, mtp2ebmtp, ebmtp2mtp ExportMethods: as.list, plot, summary, update, EBupdate, [ ExportClasses: MTP, EBMTP Package: MVCClass ExportMethods: callFun, shortName, preprocessFun, from, childUpdateDataMessage, parentUpdateDataMessage, childName, type, mData, dataName, handleMessage, modelData, modelName, linkData, virtualData, updateModel, provideInfo, modelVar, model, viewList, controller, parentMVC, childMVCList, win, winNum, plotDevice, plotPar, drArea, dfRows, xvar, yvar, clist, motionEvent, clickEvent, identifyView, updateView, redrawView, xval, yval, callFun<-, shortName<-, preprocessFun<-, from<-, childUpdateDataMessage<-, parentUpdateDataMessage<-, childName<-, type<-, mData<-, dataName<-, modelVar<-, modelData<-, modelName<-, linkData<-, virtualData<-, model<-, viewList<-, controller<-, parentMVC<-, childMVCList<-, win<-, winNum<-, plotDevice<-, plotPar<-, drArea<-, dfRows<-, xvar<-, yvar<-, clist<-, xval<-, yval<- ExportClasses: gEventFun, gAddDataMessage, gAddViewMessage, gUpdateDataMessage, gUpdateViewMessage, gAddChildMessage, gSendParentMessage, gSendChildMessage, gMessage, gModifyMessage, gAddMessage, gUpdateMessage, dfModel, gModel, MVC, singleModelMVC, linkedModelMVC, plotView, sPlotView, spreadView, genView, gAskAncestorMessage, qqPlotView Package: mygene Exports: MyGene, getGene, getGenes, query, queryMany, makeTxDbFromMyGene ExportMethods: metadata ExportClasses: MyGene Package: mzID Exports: database, evidence, files, flatten, id, idScanMap, modifications, mzID, mzIDCollection, mzIDdatabase, mzIDevidence, mzIDparameters, mzIDpeptides, mzIDpsm, parameters, peptides, removeDecoy, scans, software Package: mzR Exports: openMSfile, openIDfile ExportMethods: close, isInitialized, initializeRamp, runInfo, fileName, instrumentInfo, chromatogramsInfo, manufacturer, model, ionisation, analyzer, detector, header, peaksCount, peaks, get3Dmap, softwareInfo, sampleInfo, sourceInfo, mzidInfo, psms, modifications, substitutions, database, enzymes, tolerance, score, para ExportClasses: mzR, mzRramp, mzRnetCDF, mzRpwiz, mzRident Package: ncdfFlow Exports: as.flowSet, clone.ncdfFlowSet, getFileName, getIndices, initIndices, load_ncfs, ncdfFlowList, ncdfFlowSet, ncfsApply, read.ncdfFlowSet, save_ncfs, unlink, updateIndices ExportMethods: xyplot, updateIndices, unlink, transform, split, rbind2, phenoData, pData, ncfsApply, ncdfFlowSet, lapply, initIndices, getIndices, filter, densityplot, compensate, colnames, Subset, sampleNames<-, phenoData<-, pData<-, colnames<-, [[<-, [[, [ ExportClasses: ncdfFlowSet, ncdfFlowList Package: NCIgraph Exports: getNCIPathways, getSubtype.NCIgraph, is.NCIgraph, parseNCInetwork, translateNCI2GeneID ExportClasses: NCIgraph Package: neaGUI Exports: neaGUI, nea Package: nem Exports: BFSlevel, closest.transitive.greedy, sampleRndNetwork, sampleData, getDensityMatrix, infer.edge.type, local.model.prior, nem.bootstrap, nem.jackknife, nem.consensus, nem, nemModelSelection, nem.calcSignificance, nem.discretize, network.AIC, plotEffects, plot.nem, plot.nem.greedy, plot.nem.consensus, plot.nem.bootstrap, plot.nem.jackknife, plot.nem.greedy, plot.ModuleNetwork, plot.score, plot.pairwise, plot.triples, plot.nem.greedyMAP, plot.nem.BN, plot.mc.eminem, plot.dynoNEM, prune.graph, SCCgraph, filterEGenes, getRelevantEGenes, set.default.parameters, sim.intervention, subsets, transitive.closure, transitive.reduction, transitive.projections, enumerate.models, nem.cont.preprocess, print.nem, print.nem.greedy, print.ModuleNetwork, print.nem.greedyMAP, print.pairwise, print.triples, print.nem.jackknife, print.nem.bootstrap, print.nem.consensus, print.nem.BN, print.score, print.mc.eminem, print.dynoNEM, quicknem, prior.EgeneAttach.EB Package: netbiov Exports: plot.modules, splitg.mst, mst.plot, mst.plot.mod, plot.spiral.graph, plot.abstract.module, plot.abstract.nodes, level.plot, plot.NetworkSperical.startSet, plot.NetworkSperical, plot.netbiov Package: NetPathMiner Exports: KGML2igraph, NPMdefaults, SBML2igraph, assignEdgeWeights, biopax2igraph, colorVertexByAttr, expandComplexes, extractPathNetwork, fetchAttribute, getAttrNames, getAttrStatus, getAttribute, getGeneSetNetworks, getGeneSets, getPathsAsEIDs, layoutVertexByAttr, makeGeneNetwork, makeReactionNetwork, pathClassifier, pathCluster, pathRanker, pathsToBinary, plotAllNetworks, plotClassifierROC, plotClusterMatrix, plotClusterProbs, plotClusters, plotCytoscape, plotCytoscapeGML, plotNetwork, plotPathClassifier, plotPathCluster, plotPaths, predictPathClassifier, predictPathCluster, registerMemoryErr, rmAttribute, rmSmallCompounds, samplePaths, setAttribute, simplifyReactionNetwork, stdAttrNames, toGraphNEL, vertexDeleteReconnect Package: netresponse Exports: ICMg.combined.sampler, ICMg.get.comp.memberships, ICMg.links.sampler, P.S, P.Sr, P.r.s, P.rS, P.rs.joint, P.rs.joint.individual, P.s.individual, P.s.r, PlotMixture, PlotMixtureBivariate, PlotMixtureMultivariate, PlotMixtureUnivariate, add.ellipse, bic.mixture, bic.mixture.multivariate, bic.mixture.univariate, bic.select.best.mode, centerData, continuous.responses, detect.responses, enrichment.list.factor, enrichment.list.factor.minimal, factor.responses, factor.responses.minimal, find.similar.features, generate.toydata, get.model.parameters, independent.models, list.responses.continuous.multi, list.responses.continuous.single, list.responses.factor, list.responses.factor.minimal, list.significant.responses, listify.groupings, mixture.model, model.stats, order.responses, pick.model.pairs, pick.model.parameters, plot.data, plot.expression, plot.response, plot.responses, plot.scale, plot.subnet, read.sif, response.enrichment, response2sample, sample2response, set.breaks, vdp.mixt, vectorize.groupings, write.netresponse.results ExportMethods: getqofz, get.subnets, get.dat Package: NetSAM Exports: NetSAM Package: networkBMA Exports: networkBMA, summary.networkBMA, iBMAcontrolLM, iterateBMAlm, varord, contabs, contabs.prelim, contabs.netwBMA, matrixFormat, scores, prc, roc, writeEdges, ScanBMAcontrol, gControl, ScanBMA Package: NGScopy Exports: NGScopy, read_regions, parse_segmtype, help_segmtype, ngscopy_cmdline_example, ngscopy_unittest, df.to.gr Package: nnNorm Exports: maNormNN, detectSpatialBias, compNorm Package: NOISeq Exports: noiseq, noiseqbio, readData, addData, dat, rpkm, tmm, uqua, degenes, DE.plot, filtered.data, QCreport ExportMethods: show, explo.plot, dat2save ExportClasses: Output, Biodetection, CD, CountsBio, GCbias, lengthbias, Saturation Package: nondetects Exports: qpcrImpute Package: NormqPCR Exports: geomMean, stabMeasureM, stabMeasureRho, selectHKs, deltaCt, deltaCq, replaceNAs, deltaDeltaCt, deltaDeltaCq, makeAllNAs, makeAllNewVal, combineTechReps, combineTechRepsWithSD, replaceAboveCutOff, CqValues, ComputeNRQs Package: npGSEA Exports: getIncidence, npGSEA ExportMethods: geneSetName, stat, sigmaSq, pValues, pTwoSided, pLeft, pRight, xSet, npGSEAPlot, zStat, betaStat, alphaValue, betaValue, chiSqStat, DF, show, betaHats ExportClasses: npGSEAResultNorm, npGSEAResultNormCollection, npGSEAResultBeta, npGSEAResultBetaCollection, npGSEAResultChiSq, npGSEAResultChiSqCollection Package: NTW Exports: P.preestimation, NTW, AP.estimation.Srow, A.estimation.Srow, backward, forward, method.geo, method.sse, method.ml, comb.matrix Package: nucleR Exports: coverage.rpm, export.wig, processTilingArray, syntheticNucMap, pcKeepCompDetect, mergeCalls ExportMethods: export.bed, filterFFT, fragmentLenDetect, peakDetection, peakScoring, plotPeaks, processReads, controlCorrection Package: nudge Exports: norm1a, norm1b, norm1c, norm1d, norm2c, norm2d, nudge1, nudge2 Package: NuPoP Exports: predNuPoP, readNuPoP, plotNuPoP Package: occugene Exports: checkFormat, delta0, eMult, etDelta, fCumul, fFit, occup2Negenes, unbiasB0, unbiasDelta0, varMult Package: OCplus Exports: approx2d, average.fdr, brk2mid, CDF, CDF.paired, CDFmix, CDFmix.paired, df2var, dgfree, dmt, dmt.paired, dmtmix, dmtmix.paired, DoConstrain, DrawContourlines, EOC, FDR, FDR.paired, fdr1d, fdr2d, FDRp, gausei, lfdr, lfdr.paired, MAsim, MAsim.real, MAsim.smyth, MAsim.var, MidBreaks, MidBreaks.t, OCshow, p0, PermNull, plot.FDR.result, plot.fdr1d.result, plot.fdr2d.result, Rinv, rmatrix, samplesize, smooth1d, smooth2d.basic, smooth2d.direct, summary.fdr.result, tMixture, TOC, topDE, Tornadoplot, tstatistics, Volcanoplot Package: oligo Exports: basecontent, cleanPlatformName, read.celfiles, read.xysfiles, sequenceDesignMatrix, list.xysfiles, readSummaries, getCrlmmSummaries, getNgsColorsInfo, read.xysfiles2, read.celfiles2, basicRMA, darkColors, seqColors, seqColors2, divColors, getAffinitySplineCoefficients, getBaseProfile, basicPLM, getProbeInfo, availProbeInfo, crlmm, snprma, justSNPRMA, justCRLMM, getPD, plotM, backgroundCorrectionMethods, normalizationMethods, fitPLM, NUSE, RLE, fitProbeLevelModel, summarizationMethods ExportMethods: ncol, nprobes, nprobesets, coef, coefs.probe, weights, residuals, se, se.probe, residualSE, geometry, method, manufacturer, annotation, show, boxplot, image, paCalls, intensity, probesetNames, backgroundCorrect, normalize, summarize, normalizeToTarget, bg, bg<-, bgSequence, db, exprs, exprs<-, getContainer, getPlatformDesign, getX, getY, hist, MAplot, mm, mm<-, mmindex, mmSequence, pm, pm<-, pmChr, pmAllele, pmindex, pmFragmentLength, pmOffset, pmPosition, pmSequence, pmStrand, probeNames, rma, runDate, getNetAffx ExportClasses: oligoPLM Package: oligoClasses Exports: pdPkgFromBioC, requireAnnotation, affyPlatforms, celfileDate, celfileName, list.celfiles, is.ffmatrix, isPackageLoaded, ldStatus, ldSetOptions, parStatus, ocProbesets, ocSamples, ldPath, getBar, createFF, ocLapply, splitIndicesByLength, splitIndicesByNode, initializeBigMatrix, initializeBigVector, initializeBigArray, chromosome2integer, integer2chromosome, i2p, p2i, annotationPackages, checkExists, chromosomePositionOrder, integerArray, integerMatrix, findOverlaps, RangedDataCNV, RangedDataCBS, RangedDataHMM, library2, AssayDataList, getSequenceLengths, setCluster, getCluster, delCluster, requireClusterPkgSet, requireClusterPkg ExportMethods: featuresInRange, batch, batchNames, batchNames<-, coerce, flags, show, nu, phi, batchStatistics, batchStatistics<-, baf, lrr, baf<-, lrr<-, coverage2, findOverlaps, state, openff, closeff, checkOrder, mean, updateObject, sampleNames<-, GenomeAnnotatedDataFrameFrom, makeFeatureGRanges, clone2, getM, getA, annotatedDataFrameFrom, open, close, annotation, db, initialize, genomeBuild, geometry, kind, manufacturer, exprs, bothStrands, allele, calls, calls<-, confs, confs<-, chromosome, chromosome<-, copyNumber, copyNumber<-, cnConfidence, cnConfidence<-, elementLengths, isSnp, position, position<-, sampleNames, A, B, A<-, B<-, genomeBuild<-, getArm, numberProbes, assayDataList, dims, featureDataList ExportClasses: ff_or_matrix, AlleleSet, BeadStudioSet, oligoSnpSet, SnpSuperSet, CNSet, gSet, gSetList, RangedDataCopyNumber, RangedDataCNV, RangedDataCBS, RangedDataHMM, CopyNumberSet, GenomeAnnotatedDataFrame, BeadStudioSetList, BafLrrSetList, BafLrrSet, oligoSetList, SnpSet2, FeatureSet, ExpressionFeatureSet, SnpFeatureSet, SnpCnvFeatureSet, TilingFeatureSet, ExonFeatureSet, GeneFeatureSet, AffyTilingPDInfo, AffyExpressionPDInfo, AffySNPPDInfo, AffySNPCNVPDInfo, AffyGenePDInfo, AffyExonPDInfo, NgsExpressionPDInfo, NgsTilingPDInfo, DBPDInfo, ExpressionPDInfo, TilingPDInfo Package: OLIN Exports: anovaint, anovapin, anovaplate, anovaspatial, bas, backgroundCorrect2, colorbar.mxy, colorbar.sig, fdr.int, fdr.int2, fdr.spatial, fdr.spatial2, fgbg.visu, ino, lin, m2v, ma.matrix, ma.vector, mxy.abs.plot, mxy.plot, mxy2.plot, oin, olin, p.int, p.int2, p.spatial, p.spatial2, sig.mask, sigint.plot, sigint.plot2, sigxy.plot, sigxy.plot2, v2m Package: OLINgui Exports: OLINgui Package: omicade4 Exports: mcia, plot.mcia, plotVar, selectVar Package: OmicCircos Exports: circos, segAnglePo, sim.circos Package: OncoSimulR Exports: oncoSimulPop, oncoSimulIndiv, samplePop, plotPoset Package: oneChannelGUI Exports: as.data.frame ExportMethods: summary Package: openCyto Exports: .between_interval, cytokine, flowClust.1d, flowClust.2d, gating, gatingTemplate, listgtMethods, mindensity, prior_flowClust, quadGate.seq, quadGate.tmix, registerGatingFunction, registerPlugins, tailgate, templateGen ExportMethods: show, plot, parameters, names, getParent, getNodes, getGate, getChildren, dims, alias, add ExportClasses: ppMethod, polyFunctions, gtPopulation, gtMethod, gatingTemplate Package: OrderedList Exports: check.test.args, compareLists, getOverlap, OrderedList, overlap, plot.listComparison, plot.listComparisonOverlap, plot.OrderedList, plot.shuffledRandomScores, prepareData, preparePermutations, print.listComparison, print.listComparisonOverlap, print.OrderedList, print.shuffledRandomScores, scoreOrderComparison, scoreOrderComparisonBoth, scoreRankings, shuffledRandomScores, test.fc, test.t, test.z Package: OrganismDbi Exports: makeOrganismPackage ExportMethods: columns, keys, keytypes, select, transcripts, exons, cds, genes, transcriptsBy, exonsBy, cdsBy, metadata, seqinfo ExportClasses: OrganismDb Package: OSAT Exports: setup.sample, setup.container, create.optimized.setup, create.experiment.setup, optimal.block, optimal.shuffle, get.experiment.setup, QC, map.to.MSA, multi.barplot, multi.chisq.test, IlluminaBeadChip, GenotypingChip, IlluminaBeadChip24Plate, IlluminaBeadChip48Plate, IlluminaBeadChip96Plate, MSA4.plate, BeadChip96ToMSA4MAP, predefined ExportMethods: getLayout, initialize, plot, show, summary, metadata, metadata<-, exclude<- ExportClasses: gArray, gSlide, BeadChip, gPlate, BeadPlate, gAssembly, gContainer, gSample, gExperimentSetup Package: OutlierD Exports: OutlierD Package: PAA Exports: batchAdjust, batchFilter, diffAnalysis, loadGPR, mMsMatrix, normalizeArrays, plotFeatures, plotFeaturesHeatmap, plotMAPlots, plotNormMethods, preselect, printFeatures, pvaluePlot, selectFeatures, shuffleData, volcanoPlot Package: PADOG Exports: padog, compPADOG, filteranot Package: paircompviz Exports: transReduct, hasse, paircomp Package: PAnnBuilder Exports: getALLUrl, getALLBuilt, idBlast, createAnnObjs, pBaseBuilder_DB, pSeqBuilder_DB, crossBuilder_DB, scopBuilder_DB, subcellBuilder_DB, intBuilder_DB, InParanoidBuilder_DB, HomoloGeneBuilder_DB, PeptideAtlasBuilder_DB, dNameBuilder_DB, bfBuilder_DB, ptmBuilder_DB, GOABuilder_DB ExportMethods: dbschema Package: panp Exports: pa.calls Package: PANR Exports: assoScore, cosineSim, cosineDist ExportMethods: permNULL, fitNULL, fitBM, p2SNR, SNR2p, infer, view, summarize, viewLegend, buildPAN, viewPAN, exportPAN, sigModules, pvclustModule, viewNestedModules ExportClasses: BetaMixture, PAN Package: PAPi Exports: papi, addKeggCodes, papiHtest, papiLine, buildDatabase Package: parody Exports: calout.detect, mv.calout.detect, hamp.scale.3, tukeyor, box.scale Package: PathNet Exports: PathNet Package: pathRender Exports: rendercMAPPathway, graphcMAP, pwayRendAttrs, reduceES, plotExGraph, colorNodes ExportMethods: plot ExportClasses: pwayGraph, coloredGraph Package: pathview Exports: download.kegg, node.info, combineKEGGnodes, reaction2edge, node.map, eg2id, id2eg, cpdkegg2name, cpdname2kegg, cpd2kegg, cpdidmap, kegg.species.code, mol.sum, sim.mol.data, node.color, col.key, wordwrap, strfit, pathview, keggview.native, keggview.graph Package: paxtoolsr Exports: downloadPc, fetch, fromPsimi, getNeighbors, getPc, getPcUrl, graphPc, idMapping, integrateBiopax, mergeBiopax, pcDirections, pcFormats, pcGraphQueries, readGmt, searchPc, splitSifnx, summarize, toGSEA, toLevel3, toSBGN, toSif, toSifnx, topPathways, traverse, validate Package: Pbase Exports: rmEmptyRanges, Pparams ExportMethods: Proteins, [, [[, aa, acols, ametadata, length, metadata, pcols, pfeatures, pmetadata, pranges, pvarLabels, avarLabels, seqnames, show, cleave, plot, addIdentificationData, pfilter, proteinCoverage, proteotypic ExportClasses: Proteins, Pparams Package: pcaGoPromoter Exports: pca, print.pca, plot.pca, pcaInfoPlot, getRankedProbeIds, getRankedProbeIds.pca, GOtree, print.GOtree, plot.GOtree, GOtreeWithLeaveOut, GOtreeHits, primo, primoWithLeaveOut, primoHits, primoData Package: pcaMethods Exports: Q2, RnipalsPca, asExprSet, bpca, checkData, cvseg, kEstimate, kEstimateFast, listPcaMethods, llsImpute, nipalsPca, nlpca, nni, pca, plotPcs, ppca, prep, robustPca, robustSvd, showNniRes, showPcaRes, svdImpute, svdPca ExportMethods: wasna, slplot, scores, scl, scaled, sDev, nmissing, nVar, nPcs, nP, nObs, method, loadings, leverage, cvstat, completeObs, centered, center, R2cum, R2VX, DModX ExportClasses: pcaRes, nniRes, nlpcaNet Package: pcot2 Exports: aveExprs, aveProbe, corplot2, corplot, Cor, geneLocator, getImat, pco, pcot2, plotCor, rb, rg, t2.permu, t2, t2.unequ, wb Package: PCpheno Exports: graphTheory, overlap, complexStatus, buildFDMat, getFDgene, reduceM, densityEstimate, truncName, getDescr, KEGG2SCISI, ppiInteract ExportMethods: hyperGTest, summary, geneCounts, universeCounts, pvalues, oddsRatios, expectedCounts, universeBuilder, categoryToEntrezBuilder, plot ExportClasses: CoHyperGParams, CoHyperGResult, testResult, deResult, gtResult Package: pdInfoBuilder ExportMethods: chipName, getGeometry, makePdInfoPackage ExportClasses: AffyExpressionPDInfoPkgSeed, AffyTilingPDInfoPkgSeed, AffySNPPDInfoPkgSeed, AffySNPPDInfoPkgSeed2, AffySNPCNVPDInfoPkgSeed, AffySNPCNVPDInfoPkgSeed2, AffyExonPDInfoPkgSeed, AffyGenePDInfoPkgSeed, NgsExpressionPDInfoPkgSeed, NgsTilingPDInfoPkgSeed Package: pdmclass Exports: pdmClass, pdmGenes, pdmClass.cv, predict.pls, predict.svd Package: PECA Exports: PECA_AffyBatch, PECA_CEL, PECA_tsv Package: pepStat Exports: create_db, makeCalls, makePeptideSet, normalizeArray, plotArrayImage, plotArrayResiduals, restab, shinyPepStat, slidingMean, summarizePeptides ExportMethods: width, values, summary, subset, start, show, ranges<-, ranges, position, peptide<-, peptide, pepZscore<-, pepZscore, featureID, end, clade, [ ExportClasses: peptideSet Package: pepXMLTab Exports: pepXML2tab, PSMfilter Package: PGSEA Exports: .rwb ExportClasses: smc Package: phenoDist Exports: distToNeg, repDistRank, ctlSeparatn, clusterDist, enrichAnalysis, repCorr, PDMByWellAvg, PDMByFactorAnalysis, PDMByKS, PDMBySvmWeightVector, PDMBySvmAccuracy Package: phenoTest Exports: summary.gseaSignificanceSign, summary.gseaSignificanceVar, plot.gseaSignaturesSign, plot.gseaSignaturesVar, ExpressionPhenoTest, epheno2html, heatmapPhenoTest, ClusterPhenoTest, smoothCoxph, getEsPositions, findCopyNumber, genesInArea, gsea, getGo, getKegg, gsea.go, gsea.kegg, summary.gseaData, plot.gseaData, gsea2html, gsea.selVars, gsea.selGsets, eset2genelevel, write.html, pca ExportMethods: gseaSignatures, gseaSignificance, getEs, getEsSim, getFcHr, dim, phenoNames, p.adjust.method, approach, phenoClass, show, getMeans, getPvals, getPostProbs, getSignif, getSummaryDif, getFc, getHr, logFcHr, export2CSV, [, barplotSignatures, barplotSignifSignatures, pAdjust, getVars2test ExportClasses: epheno, gseaSignatures, gseaSignaturesSign, gseaSignaturesVar, gseaSignificanceSign, gseaSignificanceVar Package: PhenStat ExportClasses: PhenList, PhenTestResult Package: phyloseq Exports: otuTable<-, sam_data<-, sample_data<-, sampleData<-, speciesAreRows<-, taxTab<-, tre<-, access, build_tax_table, distance, DPCoA, estimate_richness, export_env_file, export_mothur_dist, filter_taxa, filterfun_sample, filterfunSample, gapstat_ord, genefilterSample, get_taxa_unique, get_variable, getSamples, getslots.phyloseq, getSpecies, getTaxa, getVariable, import_biom, import_env_file, import_mothur_dist, import_mothur, import_pyrotagger_tab, import_qiime_otu_tax, import_qiime_sample_data, import_qiime_sampleData, import_qiime, import_RDP_cluster, import_RDP_otu, import_usearch_uc, import, make_network, merge_phyloseq, merge_species, microbio_me_qiime, nodeplotblank, nodeplotboot, nodeplotdefault, nspecies, ordinate, otuTable, parse_taxonomy_default, parse_taxonomy_greengenes, parse_taxonomy_qiime, phyloseq_to_deseq2, phyloseq, plot_bar, plot_clusgap, plot_heatmap, plot_net, plot_network, plot_ordination, plot_richness_estimates, plot_richness, plot_scree, plot_taxa_bar, plot_tree, prune_species, psmelt, rank_names, rank.names, rarefy_even_depth, read_tree_greengenes, read_tree, rm_outlierf, sam_data, samData, sample_sums, sample_variables, sample.names, sample.variables, sampleData, sampleNames, sampleSums, show_mothur_cutoffs, show_mothur_list_cutoffs, species.names, speciesarerows, speciesAreRows, speciesSums, subset_ord_plot, subset_samples, subset_species, subset_taxa, tax_glom, taxa_sums, taxaplot, taxglom, taxtab, taxTab, threshrank, threshrankfun, tip_glom, tipglom, topf, topk, topp, transform_sample_counts, transformSampleCounts, tre, tree_layout ExportMethods: UniFrac, taxa_names, taxa_are_rows, tax_table, t, show, sample_names, sample_data, refseq, prune_taxa, prune_samples, plot_phyloseq, phy_tree, otu_table, ntaxa, nsamples, mt, merge_taxa, merge_samples, merge_phyloseq_pair, get_taxa, get_sample, genefilter_sample, taxa_names<-, taxa_are_rows<-, tax_table<-, sample_names<-, phy_tree<-, otu_table<-, [ ExportClasses: taxonomyTable, sample_data, phyloseq, phylo, otu_table, dist Package: piano Exports: loadMAdata, runQC, extractFactors, diffExp, polarPlot, loadGSC, runGSA, GSAsummaryTable, geneSetSummary, networkPlot, consensusScores, consensusHeatmap, runGSAhyper, GSAheatmap, writeFilesForKiwi Package: pickgene Exports: adjustlevel, chen.poly, chipnorm, dencont, dencum, denlines, do.oddsplot, em.ggb, fitgg, gammaden, holms, lod.ggb, lod.plot, lodprobes, loglik, makecont, model.pickgene, multipickgene, nlminb, nloglik, normal.richmond, npdiag, nploglik, oddsplot, orangene, pickedchisq, pickedhist, pickedpair, pickedscore, pickgene, pickgene.poly, pickgene.two, pickgene2, pmarg, predrecur, rangene, rankgene, robustbox, robustscale, s.check0, s.check1, s.check2, s.marg, shrinkplot, sixden, toprankgene, twoarray.norm, twoarray.plot, twowayanovapickgene Package: PICS Exports: segReadsList, segReadsListPE, segReadsPE, segReadsGeneric, segReads, segmentPICS, summarySeg, makeRangedDataOutput, PICS, picsFDR, newPicsError, setParaEM, setParaPrior, candidate.region, segChrRead, bam2gr ExportMethods: coerce, show, summary, plot, wigDensity, chromosome, score, se, seF, seR, sigmaSqF, sigmaSqR, mu, delta, w, code, length, K, [, [[, map, minRange, maxRange, scoreForward, scoreReverse ExportClasses: segReads, segReadsList, segReadsPE, segReadsListPE, pics, picsError, picsList Package: PING Exports: PING, postPING, newPingError, segReads, segReadsPE, segReadsList, segReadsListPE, segmentPING, NucleosomeTrack, CoverageTrack, RawReadsTrack, plotSummary, makeRangedDataOutput, setParaPrior, setParaEM, bam2gr ExportMethods: show, summary, plot, se, seF, seR, sigmaSqF, sigmaSqR, mu, delta, w, code, length, K, [, [[, as.data.frame, chromosome, score, density ExportClasses: ping, pingError, pingList Package: pint Exports: iterative.window, fixed.window, fit.cgh.mir.byname, fit.cgh.mrna.byname, get.neighboring.probes, get.neighs, join.top.regions, summarize.region.parameters, order.feature.info, pint.data, pint.match, plot.GeneDependencyModel, plot.ChromosomeModels, plot.GenomeModels, screen.cgh.mrna, screen.cgh.mir, W.effects, z.effects ExportMethods: [[, [[<-, setLoc<-, setGeneName<-, setArm<-, setChromosome<-, getW, getPhi, getScore, getLoc, getGeneName, getChromosome, getArm, getModelMethod, getParams, getPArm, getQArm, getWindowSize, getModelNumbers, topGenes, topModels, orderGenes, findModel, isEmpty, as.data.frame ExportClasses: GeneDependencyModel, ChromosomeModels, GenomeModels Package: pkgDepTools Exports: getInstallOrder, makeDepGraph Package: plateCore Exports: panel.densityplot.flowPlate, prepanel.densityplot.flowPlate, prepanel.xyplot.flowPlate, panel.xyplot.flowPlate ExportMethods: compensate, flowPlate, fixAutoFl, plateSet, phenoData, getGroups, wellAnnotation, Subset, %on%, applyControlGates, summaryStats, sampleNames, fpbind, setControlGates, plotPlate, gutterPlot, mfiPlot, densityplot, xyplot ExportClasses: flowPlate Package: plethy Exports: makeBuxcoDB, annoTable, annoCols, annoLevels, dbName, samples, variables, tables, retrieveData, addAnnotation, dbImport, summaryMeasures, retrieveMatrix, tsplot, mvtsplot, day.infer.query, break.type.query, parse.buxco, parse.buxco.basic, add.labels.by.sample, adjust.labels, get.err.breaks, proc.sanity, sample.db.path, buxco.sample.data.path ExportClasses: BuxcoDB Package: plier Exports: justPlier Package: PLPE Exports: lpe.paired, lpe.paired.default, lpe.paired.fdr, lpe.paired.fdr.default, print.lpe.paired, summary.lpe.paired, print.lpe.paired.fdr, summary.lpe.paired.fdr, am.trans.paired, base.error.paired, generate.null Package: plrs Exports: plrs.sim, plrs.cb, plrs.series, criteria, modify.conf, plrs, plrs.select, plrs.test ExportMethods: coef, fitted, effects, knots, model.matrix, plot, predict, print, residuals, show, summary ExportClasses: plrs, plrs.select, plrs.series Package: plw Exports: estimateMVbeta, estimateSigmaMVbeta, estimateSigmaMV, estimateSigma, getKnots, lmw, plw, scaleParameterPlot, topRankSummary, varHistPlot, plotSummaryLog2FC, plotSummaryT, logitTTransform, logitTStat, studenttTTest, madByIndex, meanByIndex, medianByIndex, orderStatByIndex, sdByIndex, meanSdByRow, HowToPLW Package: polyester Exports: add_error, count_transcripts, create_read_numbers, fpkm_to_counts, generate_fragments, getAttributeField, get_params, get_reads, reverse_complement, seq_gtf, simulate_experiment, simulate_experiment_countmat, write_reads Package: ppiStats Exports: assessSymmetry, bpMatrix, calcInOutDegStats, degreeEstimates, estErrProbMethodOfMoments, estimateCCMErrorRates, findAdjacent, genBPGraph, idHomodimers, idStochastic, idSystematic, idViableProteins, nullDistDoublyTestedEdges, ppiBuildParams4GO, ppiHGTest4GO, ppiBuildParams4PFAM, ppiHGTest4PFAM, twowayPERM, findDegree, makeBinVect, estimatePPIErrorRates, createSummaryTables, viabilityCharts, inOutScatterCharts, separateExptBySize, findAdjacent Package: prada Exports: analysePlate, as.all, barploterrbar, combineFrames, csApply, fitNorm2, getPradaPar, plotNorm2, devDims, plotPlate, readCytoSet, readFCS, read.fcs, removeCensored, setPradaPars, thresholds, threePanelPlot, devRes, .drawCircle, .drawPie, vpLocation, touchFCS, combineGates, progress, updateProgress, killProgress, getAlphaNumeric ExportMethods: colnames, colnames<-, description, description<-, exprs, exprs<-, length, [, [[, [[<-, pData, phenoData, phenoData<-, show, plot, gate, applyGate, drawGate, gate<-, names, names<-, as.gateSet, nrow, ncol, appendGates, lines, split ExportClasses: cytoFrame, cytoSet, gate, gateSet Package: prebs Exports: calc_prebs Package: PREDA Exports: GenomicAnnotationsFromLibrary, MergeStatisticAnnotations2DataForPREDA, PREDA_main, preprocessingGE, SODEGIRpreprocessingGE, GenomicAnnotationsFromfile, GenomicAnnotationsFromdataframe, GenomicAnnotationsForPREDAFromfile, DataForPREDAMedianCenter, StatisticsForPREDAFromfile, StatisticsForPREDAFromdataframe, GenomicRegionsFindOverlap, GenomicRegions2dataframe, GenomicRegionsFromfile, GenomicRegionsFromdataframe ExportMethods: GenomicAnnotations2dataframe, GenomicAnnotationsSortAndCleanNA, GenomicAnnotations2reference_positions, GenomicAnnotationsFilter_neg, GenomicAnnotationsFilter_pos, GenomicAnnotationsExtract, GenomicAnnotations2GenomicAnnotationsForPREDA, GenomicAnnotationsForPREDA2GenomicAnnotations, GenomicAnnotationsForPREDA2dataframe, GenomicAnnotationsForPREDA2PREDAResults, StatisticsForPREDA2dataframe, StatisticsForPREDAFilterColumns_neg, StatisticsForPREDAFilterColumns_pos, analysesNames, getStatisticByName, DataForPREDA2dataframe, DataForPREDA2GenomicAnnotationsForPREDA, DataForPREDA2StatisticsForPREDA, PREDAResults2dataframe, PREDAResults2PREDADataAndResults, PREDAResults2GenomicRegionsSingle, PREDAResults2GenomicRegions, PREDAResultsGetObservedFlags, PREDADataAndResults2dataframe, GenomicRegionsChrNumber, GenomicRegionsNumber, GenomicRegionsSpan, GenomicRegionsTotalSpan, GenomicRegionsCreateRegionsIds, GenomicRegionsComparison, GenomicRegionsAnnotate, GenomicRegionsFilter_neg, GenomicRegionsFilter_pos, eset2GenomicAnnotations, statisticsForPREDAfromEset, genomePlot, computeDatasetSignature, SODEGIR_GEstatistics ExportClasses: GenomicAnnotations, GenomicAnnotationsForPREDA, StatisticsForPREDA, DataForPREDA, PREDAResults, PREDADataAndResults, GenomicRegions Package: proBAMr Exports: PrepareAnnotationGENCODE, PSMtab2SAM Package: PROcess Exports: bslnoff, isPeak, pk2bmkr, getMzs, lnn, quality, sigma, getPeaks, noise, read.files, specZoom, intg, peaks, rmBaseline, renorm, binning, gelmap, aveSpec, align, getPeaks2, avesd, is.multiple Package: procoil Exports: readCCModel ExportMethods: predict, show, plot, weights, profile ExportClasses: CCModel, CCProfile Package: ProCoNA Exports: proconaVersionFun, buildProconaNetwork, bootstrapProconaNetwork, subsetPeptideData, modulePhenotypeCorrelations, moduleMemberCorrelations, toPermTest, peptideConnectivityTest, peptideCorrelationTest, goStatTest, ppiPermTest, getFisherMatrix, compareNetworksWithFishersExactTest, compareNetworksWithFishersExactTestProcona, correlationWithPhenotypesHeatMap, MMvsPS, MMvsPSallModules, corBootstrap, utri, plotNet, printNet, networkName, networkName<-, samples, samples<-, peptides, peptides<-, proconaVersion, proconaVersion<-, networkName, networkName<-, networkType, networkType<-, adj, adj<-, TOM, TOM<-, pepTree, pepTree<-, mergedMEs, mergedMEs<-, mergedColors, mergedColors<-, MEs, MEs<-, dynamicColors, dynamicColors<-, networkPower, networkPower<-, permtest, permtest<-, colorOrder, colorOrder<- ExportClasses: proconaNet Package: pRoloc Exports: markerMSnSet, unknownMSnSet, sampleMSnSet, testMSnSet, getPredictions, getMarkers, minClassScore, testMarkers, minMarkers, addMarkers, pRolocmarkers, empPvalues, getStockcol, getStockpch, setStockcol, setStockpch, getUnknowncol, getUnknownpch, setUnknowncol, setUnknownpch, plot2D, addLegend, plotDist, highlightOnPlot, plsdaRegularisation, plsdaOptimisation, plsdaOptimization, plsdaPrediction, plsdaClassification, svmRegularisation, svmOptimisation, svmOptimization, svmPrediction, svmClassification, ksvmRegularisation, ksvmOptimisation, ksvmOptimization, ksvmPrediction, ksvmClassification, knnRegularisation, knnOptimisation, knnOptimization, knnPrediction, knnClassification, nbRegularisation, nbOptimisation, nbOptimization, nbPrediction, nbClassification, nnetRegularisation, nnetOptimisation, nnetOptimization, nnetPrediction, nnetClassification, perTurboOptimisation, perTurboOptimization, perTurboClassification, getParams, getRegularisedParams, getRegularizedParams, rfRegularisation, rfOptimisation, rfOptimization, rfPrediction, rfClassification, phenoDisco, makeNaData, makeNaData2, whichNA, lopims, lopims1, lopims2, lopims3, lopims4, lopims5 ExportMethods: chi2, show, MLearn, getWarnings, getSeed, getF1Scores, f1Count, levelPlot, plot, nndist ExportClasses: GenRegRes Package: pRolocGUI Exports: pRolocVis, pRolocComp Package: PROMISE Exports: PROMISE, avg.abs.genestat, jung.rstat, spearman.rstat, promise.genestat Package: prot2D Exports: ES.prot, Norm.qt, Norm.vsn, RIplot, Sim.Prot.2D, efronT.Prot, modT.Prot, samT.Prot, shrinkT.Prot, ttest.Prot, robust.fdr Package: proteinProfiles Exports: filterFeatures, grepAnnotation, profileDistance, plotProfileDistance Package: proteoQC Exports: msQCpipe, reportHTML, showEnzyme, showMods, print.msQCres, loadmsQCres, calcMSQCMetrics, chargeStat, labelRatio, proteinGroup Package: PSEA Exports: marker, crplot, em_quantvg, swlm, fmm, lmfitst, slt, pvalmat, coefmat Package: PSICQUIC Exports: PSICQUIC, IDMapper, interactionTypes, detectionMethods, speciesIDs ExportMethods: interactions, providers, rawQuery, addGeneInfo, addStandardNames, show ExportClasses: PSICQUIC, IDMapper Package: Pviz Exports: ATrack, CladeTrack, DTrack, ProbeTrack, ProteinAxisTrack, ProteinSequenceTrack, plot_clade, plot_inter ExportClasses: ProteinSequenceTrack, ProteinAxisTrack, ProbeTrack, DTrack, CladeTrack, ATrack Package: PWMEnrich Exports: getBackgroundFrequencies, makeBackground, makePriors, makePWMCutoffBackground, makePWMEmpiricalBackground, makePWMGEVBackground, makePWMLognBackground, makePWMPvalCutoffBackground, makePWMPvalCutoffBackgroundFromSeq, motifDiffEnrichment, motifEcdf, motifEnrichment, motifIC, motifScores, motifSimilarity, PFMtoPWM, plotMotifScores, plotMultipleMotifs, PWMUnscaled, readMotifs, registerCoresPWMEnrich, scanWithPWM, seqLogoGrid, useBigMemoryPWMEnrich, toPWM ExportMethods: sequenceReport, reverseComplement, plotTopMotifsSequence, plotTopMotifsGroup, plot, motifRankingForSequence, motifRankingForGroup, groupReport, as.data.frame ExportClasses: PWMLognBackground, PWMGEVBackground, PWMEmpiricalBackground, PWMCutoffBackground, PWM, MotifEnrichmentResults, MotifEnrichmentReport Package: qcmetrics Exports: QcMetric, QcMetrics, QcMetadata, qcshow, as.data.frame.QcMetrics, Qc2Tex, Qc2Tex2, Qc2Tex3, Qc2Rmd, rnadeg, n15qc ExportMethods: status, status<-, name, name<-, qcdata, qcdata<-, qcenv, qcenv<-, metadata, metadata<-, mdata, mdata<-, names, names<-, show, plot, print, show<-, plot<-, [, [[, qcReport ExportClasses: QcMetric, QcMetrics, QcMetadata Package: QDNAseq Exports: addPhenodata, applyFilters, binReadCounts, callBins, compareToReference, correctBins, downloadBinAnnotations, estimateCorrection, exportBins, frequencyPlot, getBinAnnotations, highlightFilters, isobarPlot, makeCgh, noisePlot, normalizeBins, normalizeSegmentedBins, plot, poolRuns, segmentBins, smoothOutlierBins, createBins, calculateMappability, calculateBlacklist, iterateResiduals, chromosomes, bpstart, bpend ExportClasses: QDNAseqReadCounts, QDNAseqCopyNumbers Package: qpcrNorm Exports: calcCV, ctQc, matrixByPlate, normQpcrHouseKeepingGenes, normQpcrQuantile, normQpcrRankInvariant, plotVarMean, readQpcr, readQpcrBatch, writeQpcr ExportClasses: qpcrBatch Package: qpgraph Exports: qpHist, qpGraphDensity, qpCliqueNumber, qpClique, qpBoundary, qpAnyGraph, qpGetCliques, qpUpdateCliquesRemoving, qpIPF, qpHTF, qpPAC, qpPCC, qpRndGraph, qpRndWishart, qpG2Sigma, qpUnifRndAssociation, qpK2ParCor, qpPrecisionRecall, qpPRscoreThreshold, qpImportNrr, qpTopPairs, qpPlotNetwork, qpPlotMap, qpCov, erGraphParam, dRegularGraphParam, erMarkedGraphParam, dRegularMarkedGraphParam, eQTLcrossParam, eQTLnetworkEstimationParam ExportMethods: qpNrr, qpAvgNrr, qpGenNrr, qpGraph, qpPAC, qpPCC, qpCItest, qpAllCItests, qpEdgeNrr, qpEdgeCor, qpFunctionalCoherence, show, determinant, dim, dimnames, summary, rmvnorm, rcmvnorm, sim.cross, plot, rgraphBAM, UGgmm, HMgmm, rUGgmm, rHMgmm, $, eQTLcross, reQTLcross, addGenes, addeQTL, addGeneAssociation, alleQTL, ciseQTL, transeQTL, allGeneAssociations, geneticMap, physicalMap, graph, ggData, markerNames, geneNames, geneAnnotation, eQTLnetworkEstimate, varExplained, resetCutoffs ExportClasses: SsdMatrix, erGraphParam, dRegularGraphParam, erMarkedGraphParam, dRegularMarkedGraphParam, UGgmm, HMgmm, eQTLcross, eQTLcrossParam, eQTLnetworkEstimationParam, eQTLnetwork, qpGraph Package: qrqc Exports: readSeqFile, makeReport, getBase, getKmer, getBaseProp, getQual, getGC, getMCQual, getSeqlen, basePlot, qualPlot, seqlenPlot, gcPlot, geom_qlinerange, list2df, scale_color_iupac, scale_color_dna, kmerKLPlot, kmerEntropyPlot, calcKL, plotQuals, plotBases, plotSeqLengths, plotGC Package: QUALIFIER Exports: htmlReport<-, qpar<-, rFunc<-, scatterPar<-, clearCheck, getQAStats, htmlReport, initDB, load_db, outlier.cutoff, outlier.norm, outlier.t, proportion.outliers.mle, proportion.outliers.robust, qaPreprocess, qoutlier, qpar, queryStats, rFunc, read.qaTask, rlm, saveToDB, save_db, scatterPar ExportMethods: qaReport, qaCheck, plot ExportClasses: qaTask Package: quantro Exports: MSbetween, MSwithin, anova, matboxplot, matdensity, quantro, quantroPlot, quantroPvalPerm, quantroStat, quantroStatPerm, summary ExportMethods: summary, quantroStatPerm, quantroStat, quantroPvalPerm, anova, MSwithin, MSbetween ExportClasses: quantro Package: quantsmooth Exports: quantsmooth, quantsmooth.seg, quantsmooth.cv, getLambdaMin, plotSmoothed, getChangedRegions, getChangedIdx, numericCHR, characterCHR, scaleto, plotChromosome, prepareGenomePlot, paintCytobands, lengthChromosome, drawSimpleChrom, position2Cytoband, grid.chromosome Package: QuasR Exports: qAlign, qCount, preprocessReads, qExportWig, qQCReport, qMeth, alignmentStats, qProfile ExportMethods: length, genome, auxiliaries, alignments, [, show ExportClasses: qProject Package: qusage Exports: qusage, makeComparison, aggregateGeneSet, calcVIF, oneWay.pVal, pdf.pVal, twoWay.pVal, twoCurve.pVal, getXcoords, calcBayesCI, newQSarray, qsTable, numFeatures, numPathways, plotGeneSetDistributions, plotDensityCurves, plotCIs, plotCIsGenes, read.gmt ExportMethods: plot, print, dim, head, summary, [<- ExportClasses: QSarray Package: qvalue Exports: plot.qvalue, qplot, qsummary, qvalue, qwrite, summary.qvalue Package: r3Cseq Exports: getCoverage, expCoverage, contrCoverage, getRawReads, expRawData, expRawData<-, contrRawData, contrRawData<-, getBatchRawReads, getReadCountPerRestrictionFragment, getBatchReadCountPerRestrictionFragment, getReadCountPerWindow, getBatchReadCountPerWindow, getViewpoint, calculateRPM, calculateBatchRPM, expReadCount, contrReadCount, expRPM, contrRPM, getInteractions, getBatchInteractions, expInteractionRegions, contrInteractionRegions, plotOverviewInteractions, plotInteractionsNearViewpoint, plotInteractionsPerChromosome, plotDomainogramNearViewpoint, plot3Cecdf, export3CseqRawReads2bedGraph, export3Cseq2bedGraph, exportInteractions2text, exportBatchInteractions2text, generate3CseqReport, getExpInteractionsInRefseq, getContrInteractionsInRefseq ExportClasses: r3Cseq, r3CseqInBatch Package: R453Plus1Toolbox Exports: extendedCIGARToList, listToExtendedCIGAR, readSFF, writeSFF, qualityReportSFF ExportMethods: alignShortReads, readsOnTarget, coverageOnTarget, calculateTiTv, genomeSequencerMIDs, sequenceCaptureLinkers, demultiplexReads, removeLinker, filterChimericReads, detectBreakpoints, mergeBreakpoints, annotateVariants, annotatedVariants, htmlReport, ava2vcf, plotVariationFrequency, plotAmpliconCoverage, plotVariants, plotChimericReads, seqsC1, seqsC1<-, seqsC2, seqsC2<-, commonBpsC1, commonBpsC1<-, commonBpsC2, commonBpsC2<-, commonAlignC1, commonAlignC1<-, commonAlignC2, commonAlignC2<-, alignedReadsC1, alignedReadsC1<-, alignedReadsC2, alignedReadsC2<-, MapperSet, AVASet, fDataAmp, featureDataAmp, featureDataAmp<-, assayDataAmp, assayDataAmp<-, getAlignedReads, referenceSequences, referenceSequences<-, getReadStatus, getVariantPercentages, setVariantFilter, name, name<-, flowgramFormat, flowgramFormat<-, flowChars, flowChars<-, keySequence, keySequence<-, clipQualityLeft, clipQualityLeft<-, clipQualityRight, clipQualityRight<-, clipAdapterLeft, clipAdapterLeft<-, clipAdapterRight, clipAdapterRight<-, flowgram, flowgram<-, flowgrams, flowgrams<-, flowIndexes, flowIndexes<-, read, read<-, quality, quality<-, reads, reads<-, addRead, getRead, sff2fastq, readLengthStats, readLengthHist, baseQualityStats, baseQualityHist, sequenceQualityHist, positionQualityBoxplot, baseFrequency, nucleotideCharts, gcContent, gcPerPosition, gcContentHist, complexity.dust, complexity.entropy, dinucleotideOddsRatio, flowgramBarplot, homopolymerHist ExportClasses: AVASet, MapperSet, AnnotatedVariants, Breakpoints, SFFRead, SFFContainer Package: rain Exports: rain Package: rama Exports: arrange.row, est.shift, fit.model, is.row.na, ls.effect, mat.mean, ratio.plot, weight.plot Package: RamiGO Exports: agraph, adjMatrix, annot, relations, leaves ExportClasses: AmigoDot Package: randPack Exports: getTreatment, getEnrolleeInfo, createTrial, validPID, makeRandomizer, treatmentFactors, factorNames, treatmentNames, numberOfTreatments, treatmentFactors, numberOfFactorLevels, minimizeTaves, minimizePocSim, simPats ExportMethods: randomization<- ExportClasses: ClinicalExperiment, ClinicalTrial, PatientData, PatientID, Randomizer, RandomizerDesc Package: RankProd Exports: NaReplace, NaReplace2, Newdata, NewdataCom, OriginxyCall, OriginxyCall2, plotGene, plotRP, RankComp, RankProd1, RankProd2, RankSum, RP, RPadvance, RSadvance, topGene, xyCall Package: Rariant Exports: acCi, nhsCi, scoreTest, nmTest, feTest, ciOutside, ciCovers, ciOverlap, ciWidth, plotConfidenceIntervals, plotAbundanceShift, coverageProbability, ciAdjustLevel, rariant, rariantStandalone, pos2gr, gr2pos, readRariant, writeRariant, rariantInspect, splitSampleBinom, tallyBamRegion, eventFillScale, verdictColorScale, rateFillScale, baseFillScale, yesNoMaybe, updateCalls, mergeCalls, filterCalls, findCalls, evidenceHeatmap, tallyPlot Package: RBGL Exports: articulationPoints, astarSearch, aver.wavefront, bandwidth, bellman.ford.sp, betweenness.centrality.clustering, biConnComp, boyerMyrvoldPlanarityTest, brandes.betweenness.centrality, chrobakPayneStraightLineDrawing, circle.layout, circleLayout, clusteringCoef, clusteringCoefAppr, connectedComp, cuthill.mckee.ordering, dag.sp, dijkstra.sp, dominatorTree, edgeConnectivity, edmondsOptimumBranching, edmondsMaxCardinalityMatching, edmonds.karp.max.flow, extractPath, floyd.warshall.all.pairs.sp, fruchtermanReingoldForceDirectedLayout, gprofile, graphGenerator, gursoyAtunLayout, highlyConnSG, incremental.components, init.incremental.components, isKuratowskiSubgraph, isomorphism, isStraightLineDrawing, is.triangulated, ith.wavefront, johnson.all.pairs.sp, kamada.kawai.spring.layout, kamadaKawaiSpringLayout, kCliques, kCores, kingOrdering, kolmogorov.max.flow, lambdaSets, lengauerTarjanDominatorTree, makeBiconnectedPlanar, makeConnected, makeMaximalPlanar, maxClique, maximumCycleRatio, maxWavefront, minCut, minDegreeOrdering, minimumCycleRatio, mstree.kruskal, mstree.prim, planarCanonicalOrdering, planarFaceTraversal, prim.minST, push.relabel.max.flow, randomGraphLayout, removeSelfLoops, rms.wavefront, same.component, separates, sequential.vertex.coloring, sloan.ordering, sloanStartEndVertices, sp.between, sp.between.scalar, strongComp, transitive.closure, transitivity, tsort ExportMethods: bfs, dfs Package: RBioinf Exports: simpleSort, simpleRand, asSimpleVector, Rcal, subClassNames, superClassNames, simplePVect, LPO, superClasses, class2Graph, S4Help, computeClassLinearization, randDNA, subsetAsCharacter, setVNames, convertMode, printWithNumbers, classList2Graph, traceMethods Package: rBiopaxParser Exports: CLASS_INHERITANCE_BP2, CLASS_INHERITANCE_BP3, CLASS_PROPERTIES_BP2, CLASS_PROPERTIES_BP3, DATABASE_BIOPAX, addBiochemicalReaction, addBiopaxInstance, addBiopaxInstances, addControl, addPathway, addPathwayComponents, addPhysicalEntity, addPhysicalEntityParticipant, addPropertiesToBiopaxInstance, calcGraphOverlap, colorGraphNodes, combineNodes, createBiopax, diffGraphs, downloadBiopaxData, generateNewUniqueID, getClassProperties, getInstanceClass, getInstanceProperty, getNeighborhood, getReferencedIDs, getReferencingIDs, getSubClasses, getSuperClasses, getXrefAnnotations, hasProperty, intersectGraphs, isOfClass, layoutRegulatoryGraph, listComplexComponents, listInstances, listInteractionComponents, listPathwayComponents, listPathways, mergePathways, pathway2AdjacancyMatrix, pathway2Geneset, pathway2RegulatoryGraph, plotRegulatoryGraph, readBiopax, removeInstance, removeNodes, removeProperties, selectInstances, splitComplex, transitiveClosure, transitiveReduction, uniteGraphs, writeBiopax Package: rbsurv Exports: rbsurv, rbsurv.default Package: Rcade Exports: RcadeAnalysis, defineBins, countReads, diffCountsBaySeq, constructRcadeTable ExportMethods: plotMM, plotBB, plotBBB, plotPCA, exportRcade, getDE, getChIP, getRcade, getDE<-, getChIP<-, getRcade<- ExportClasses: Rcade, RcadeTrack Package: Rchemcpp Exports: createRMolecule, getMoleculeNamesFromSDF, getMoleculePropertyFromSDF, readRmoleculeset, sd2gram, sd2gram3Dpharma, sd2gram3Dspectrum, sd2gramSpectrum, sd2gramSubtree Package: RchyOptimyx Exports: RchyOptimyx, summary, plot, merge Package: Rcpi Exports: acc, calcDrugFPSim, calcDrugMCSSim, calcParProtGOSim, calcParProtSeqSim, calcTwoProtGOSim, calcTwoProtSeqSim, checkProt, convMolFormat, extractDrugAIO, extractDrugALOGP, extractDrugAminoAcidCount, extractDrugApol, extractDrugAromaticAtomsCount, extractDrugAromaticBondsCount, extractDrugAtomCount, extractDrugAutocorrelationCharge, extractDrugAutocorrelationMass, extractDrugAutocorrelationPolarizability, extractDrugBCUT, extractDrugBPol, extractDrugBondCount, extractDrugCPSA, extractDrugCarbonTypes, extractDrugChiChain, extractDrugChiCluster, extractDrugChiPath, extractDrugChiPathCluster, extractDrugDescOB, extractDrugECI, extractDrugEstate, extractDrugEstateComplete, extractDrugExtended, extractDrugExtendedComplete, extractDrugFMF, extractDrugFragmentComplexity, extractDrugGraph, extractDrugGraphComplete, extractDrugGravitationalIndex, extractDrugHBondAcceptorCount, extractDrugHBondDonorCount, extractDrugHybridization, extractDrugHybridizationComplete, extractDrugHybridizationRatio, extractDrugIPMolecularLearning, extractDrugKR, extractDrugKRComplete, extractDrugKappaShapeIndices, extractDrugKierHallSmarts, extractDrugLargestChain, extractDrugLargestPiSystem, extractDrugLengthOverBreadth, extractDrugLongestAliphaticChain, extractDrugMACCS, extractDrugMACCSComplete, extractDrugMDE, extractDrugMannholdLogP, extractDrugMomentOfInertia, extractDrugOBFP2, extractDrugOBFP3, extractDrugOBFP4, extractDrugOBMACCS, extractDrugPetitjeanNumber, extractDrugPetitjeanShapeIndex, extractDrugPubChem, extractDrugPubChemComplete, extractDrugRotatableBondsCount, extractDrugRuleOfFive, extractDrugShortestPath, extractDrugShortestPathComplete, extractDrugStandard, extractDrugStandardComplete, extractDrugTPSA, extractDrugVABC, extractDrugVAdjMa, extractDrugWHIM, extractDrugWeight, extractDrugWeightedPath, extractDrugWienerNumbers, extractDrugXLogP, extractDrugZagrebIndex, extractPCMBLOSUM, extractPCMDescScales, extractPCMFAScales, extractPCMMDSScales, extractPCMPropScales, extractPCMScales, extractProtAAC, extractProtAPAAC, extractProtCTDC, extractProtCTDD, extractProtCTDT, extractProtCTriad, extractProtDC, extractProtGeary, extractProtMoran, extractProtMoreauBroto, extractProtPAAC, extractProtPSSM, extractProtPSSMAcc, extractProtPSSMFeature, extractProtQSO, extractProtSOCN, extractProtTC, getCPI, getDrug, getFASTAFromKEGG, getFASTAFromUniProt, getMolFromCAS, getMolFromChEMBL, getMolFromDrugBank, getMolFromKEGG, getMolFromPubChem, getPDBFromRCSBPDB, getPPI, getProt, getSeqFromKEGG, getSeqFromRCSBPDB, getSeqFromUniProt, getSmiFromChEMBL, getSmiFromDrugBank, getSmiFromKEGG, getSmiFromPubChem, readFASTA, readMolFromSDF, readMolFromSmi, readPDB, searchDrug, segProt Package: RCytoscape Exports: CytoscapeConnection, new.CytoscapeWindow, CytoscapeWindow, existing.CytoscapeWindow, noa.names, noa, eda.names, eda, cy2.edge.names, getAdjacentEdgeNames, makeSimpleGraph, demoSimpleGraph, makeRandomGraph, initNodeAttribute, initEdgeAttribute ExportMethods: deleteWindow, deleteAllWindows, displayGraph, predictTimeToDisplayGraph, getArrowShapes, getLayoutNames, getLayoutNameMapping, getLayoutPropertyNames, getLayoutPropertyType, getLayoutPropertyValue, setLayoutProperties, saveLayout, restoreLayout, getLineStyles, getNodeShapes, getDirectlyModifiableVisualProperties, getAttributeClassNames, getWindowCount, getWindowID, getWindowList, layoutNetwork, setNodePosition, getNodePosition, getNodeSize, ping, redraw, setTooltipInitialDelay, setTooltipDismissDelay, raiseWindow, setWindowSize, getZoom, setZoom, setCenter, getCenter, showGraphicsDetails, fitContent, fitSelectedContent, getViewCoordinates, sendNodes, sendEdges, setNodeAttributes, setNodeAttributesDirect, setEdgeAttributes, setEdgeAttributesDirect, addCyNode, addCyEdge, addGraphToGraph, dockPanel, floatPanel, hidePanel, hideAllPanels, setDefaultNodeShape, setDefaultNodeColor, setDefaultNodeSize, setDefaultNodeBorderColor, setDefaultNodeBorderWidth, setDefaultNodeFontSize, setDefaultNodeLabelColor, setDefaultEdgeLineWidth, setDefaultEdgeColor, setDefaultEdgeFontSize, setNodeTooltipRule, setEdgeTooltipRule, setNodeLabelRule, setEdgeLabelRule, setNodeColorRule, setNodeOpacityRule, setNodeBorderColorRule, setNodeBorderWidthRule, setNodeShapeRule, setNodeSizeRule, setEdgeLineStyleRule, setEdgeLineWidthRule, setEdgeTargetArrowRule, setEdgeSourceArrowRule, setEdgeTargetArrowColorRule, setEdgeSourceArrowColorRule, setEdgeColorRule, setEdgeOpacityRule, setEdgeOpacityDirect, setNodeSizeDirect, setNodeWidthDirect, setNodeHeightDirect, setNodeLabelDirect, setNodeFontSizeDirect, setNodeLabelColorDirect, setNodeShapeDirect, setNodeImageDirect, setNodeColorDirect, setNodeBorderWidthDirect, setNodeOpacityDirect, setNodeFillOpacityDirect, setNodeBorderOpacityDirect, setNodeBorderColorDirect, setNodeLabelOpacityDirect, setEdgeColorDirect, setEdgeLabelDirect, setEdgeFontSizeDirect, setEdgeLabelColorDirect, setEdgeTooltipDirect, setEdgeLineWidthDirect, setEdgeLineStyleDirect, setEdgeSourceArrowShapeDirect, setEdgeTargetArrowShapeDirect, setEdgeSourceArrowColorDirect, setEdgeTargetArrowColorDirect, setEdgeLabelOpacityDirect, setEdgeSourceArrowOpacityDirect, setEdgeTargetArrowOpacityDirect, setEdgeLabelWidthDirect, getNodeCount, getEdgeCount, getNodeAttribute, getAllNodeAttributes, getEdgeAttribute, getAllEdgeAttributes, getNodeAttributeNames, getEdgeAttributeNames, deleteNodeAttribute, deleteEdgeAttribute, getAllNodes, getAllEdges, clearSelection, selectNodes, invertNodeSelection, deleteSelectedNodes, getSelectedNodes, getSelectedNodeCount, selectEdges, getSelectedEdges, getSelectedEdgeCount, hideSelectedEdges, invertEdgeSelection, deleteSelectedEdges, createWindowFromSelection, getFirstNeighbors, selectFirstNeighborsOfSelectedNodes, sfn, getGraph, setGraph, hideNodes, hideSelectedNodes, unhideAll, pluginVersion, msg, clearMsg, getGraphFromCyWindow, getVisualStyleNames, copyVisualStyle, setVisualStyle, lockNodeDimensions, getDefaultBackgroundColor, setDefaultBackgroundColor, getDefaultNodeSelectionColor, setDefaultNodeSelectionColor, getDefaultNodeReverseSelectionColor, setDefaultNodeReverseSelectionColor, getDefaultEdgeSelectionColor, setDefaultEdgeSelectionColor, getDefaultEdgeReverseSelectionColor, setDefaultEdgeReverseSelectionColor, saveImage, saveNetwork ExportClasses: CytoscapeWindowClass, CytoscapeConnectionClass Package: RDAVIDWebService Exports: as ExportMethods: upsideDown, universeMappedCount, universeCounts, uniqueIds, type, terms, summary, subset, species, show, setTimeOut, setHttpProtocolVersion, setEmail, setCurrentSpecies, setCurrentGeneListPosition, setCurrentBackgroundPosition, setAnnotationCategories, popTotals, popHits, plot2D, percentages, membership, members, listTotals, is.connected, initialize, ids, getTimeOut, getStub, getSpecieNames, getListName, getIdTypes, getHttpProtocolVersion, getGeneListReportFile, getGeneListReport, getGeneListNames, getGeneCategoriesReport, getFunctionalAnnotationTableFile, getFunctionalAnnotationTable, getFunctionalAnnotationChartFile, getFunctionalAnnotationChart, getEmail, getDefaultCategoryNames, getCurrentSpeciesPosition, getCurrentGeneListPosition, getCurrentBackgroundListPosition, getClusterReportFile, getClusterReport, getBackgroundListNames, getAnnotationSummary, getAllAnnotationCategoryNames, genes, foldEnrichments, fdrs, enrichment, duplicateIds, dictionary, counts, connect, cluster, categories, bonferronis, benjaminis, addList, DAVIDTermCluster, DAVIDGenes, DAVIDGeneCluster, DAVIDGODag, DAVIDFunctionalAnnotationTable, DAVIDFunctionalAnnotationChart ExportClasses: DAVIDTermCluster, DAVIDResult, DAVIDGenes, DAVIDGeneCluster, DAVIDGODag, DAVIDFunctionalAnnotationTable, DAVIDFunctionalAnnotationChart, DAVIDCluster Package: Rdisop Exports: addMolecules, decomposeIsotopes, decomposeMass, getMass, getFormula, getIsotope, getValid, getMolecule, getScore, initializeCHNOPS, initializeCHNOPSMgKCaFe, initializeCHNOPSNaK, initializeElements, initializePSE, initializeCharges, isotopeScore, subMolecules Package: RDRToolbox Exports: Isomap, LLE, generateData, plotDR, SwissRoll, DBIndex Package: ReactomePA Exports: cnetplot, enrichMap, enrichPathway, gsePathway, gseaplot, viewPathway Package: ReadqPCR Exports: read.taqman, read.qPCR, checkValidTaqmanFilenames, checkValidqPCRFilename, exprs.well.order, exprs.well.order<-, read.LC480, read.LC480SampleInfo, qpcR2CyclesSet, effs, effs<-, se.effs, se.effs<- ExportMethods: merge ExportClasses: qPCRBatch, CyclesSet Package: RedeR Exports: RedPort, gtoy.rm, att.setv, att.sete, att.mapv, att.mape, subg, cea ExportMethods: calld, ping, version, updateGraph, getGraph, addGraph, addSeries, duplicateGraph, addSubgraph, addSubgraph.list, addLegend.color, addLegend.size, addLegend.shape, relax, getNodes, getNodeIDs, addNodes, deleteNodes, nestNodes, nesthc, updateContainerSize, mergeOutEdges, getContainerComponets, mergeNodes, getEdges, getEdgeIDs, getSourceEdgeIDs, getTargetEdgeIDs, setArrowDirection, addEdges, deleteEdges, addEdgeBetweenContainers, selectEdges, selectNodes, selectAllEdges, selectAllNodes, selectGraph, deSelectEdges, deSelectNodes, deSelectGraph, deleteSelectedEdges, deleteSelectedNodes, isDynamicsActive, exitd, resetd ExportClasses: RedPort Package: REDseq Exports: buildREmap, assignSeq2REsite, binom.test.REDseq, compareREDseq, distanceHistSeq2RE, summarizeByRE, plotCutDistribution, summarizeBySeq Package: RefNet Exports: RefNet, pubmedAbstract, detectDuplicateInteractions, pickBestFromDupGroup ExportMethods: interactions, providerClasses, providers, show ExportClasses: RefNet Package: RefPlus Exports: colMedians, normalize.quantiles2, rma.para, rmaplus, rmaref.predict Package: regionReport Exports: derfinderReport, derfinder_report Package: Repitools ExportMethods: show ExportClasses: FastQC, SequenceQC, SequenceQCSet, ScoresList, ClusteredScoresList, QdnaData, BayMethList Package: ReportingTools Exports: HTMLReport, CSVFile, DataPackage, validConnection, reporting.theme.alternate, reporting.theme, makeDESeqDF, readReport, fileHandlers, connectionHandlers, knitrHandlers, shinyHandlers, fileWIndexHandlers, makeOldHTMLReport, custHeaderPanel ExportMethods: publish, name, title, title<-, reportDirectory, reportDirectory<-, filename, path, url, page, page<-, finish, show, basePath, baseUrl, dependencies, dependencies<-, modifyReportDF, objectToHTML, toReportDF, Link ExportClasses: DataPackage, CSVFile, HTMLReport, BaseReport, HTMLReportRef, ReportHandlers Package: ReQON Exports: ReQON, ReadPosErrorPlot, QualFreqPlot, FWSEplot Package: rfPred ExportMethods: rfPred_scores Package: rGADEM Exports: GADEM, readPWMfile ExportMethods: dim, names, consensus, parameters, startPos, endPos, nOccurrences, nMotifs, plot, getPWM ExportClasses: parameters, align, gadem, motif Package: RGalaxy Exports: galaxy, functionToGalaxify, anotherTestFunction, GalaxyConfig, GalaxyOutput, getFriendlyName, GalaxyInputFile, testFunctionWithSelect, testFunctionWithGalaxySelectParam, RserveConnection, GalaxyIntegerParam, GalaxyNumericParam, GalaxyCharacterParam, GalaxyLogicalParam, GalaxySelectParam, gstop, gwarning, gmessage, runFunctionalTest, probeLookup, addTwoNumbers, addTwoNumbersWithTest ExportClasses: GalaxyIntegerParam, GalaxyNumericParam, GalaxyCharacterParam, GalaxyLogicalParam, GalaxySelectParam, RserveConnection, GalaxyConfig, GalaxyOutput, GalaxyInputFile Package: Rgraphviz Exports: agopen, agopenSimple, agread, agwrite, buildEdgeList, buildNodeList, checkAttrs, drawAgNode, drawTxtLabel, getDefaultAttrs, getNodeLabels, getNodeNames, graphvizVersion, graphvizCapabilities, graphLayout, makeNodeAttrs, pieGlyph, removedEdges, toFile, layoutGraph ExportMethods: graphDataDefaults, graphDataDefaults<-, graphData, graphData<-, clusterData, clusterData<-, nodeDataDefaults, nodeDataDefaults<-, nodeData, nodeData<-, edgeDataDefaults, edgeDataDefaults<-, edgeData, edgeData<-, AgEdge<-, AgEdge, AgNode<-, AgNode, agraph, arrowhead, arrowsize, arrowtail, bezierPoints, bLines, botLeft, boundBox, color, cPoints, edgemode, edgeNames, ep, fillcolor, from, getNodeCenter, getNodeHeight, getNodeLW, getNodeRW, getNodeXY, getPoints, getSpline, getX, getY, head, labelColor, labelFontsize, labelJust, labelLoc, labelText, labelWidth, laidout, layoutType, lines, name, numSplines, plot, pointList, shape, show, sp, splines, style, tail, to, toDot, txtLabel, upRight, renderGraph ExportClasses: AgEdge, AgNode, AgTextLabel, BezierCurve, boundingBox, pEdge, pNode, Ragraph, xyPoint Package: RGSEA Exports: RGSEAsd, RGSEApredict, RGSEAfix Package: rhdf5 Exports: H5open, H5close, H5garbage_collect, H5get_libversion, H5Acreate, H5Aopen, H5Aopen_by_name, H5Aopen_by_idx, H5Aexists, H5Aclose, H5Adelete, H5Aget_name, H5Aget_space, H5Aget_type, H5Aread, H5Awrite, H5Dclose, H5Dcreate, H5Dget_type, H5Dget_space, H5Dopen, H5Dread, H5Dwrite, H5Dset_extent, H5Fclose, H5Fcreate, H5Fflush, H5Fopen, H5Fis_hdf5, H5Fget_filesize, H5Fget_name, H5Gclose, H5Gcreate, H5Gcreate_anon, H5Gget_info, H5Gget_info_by_idx, H5Gget_info_by_name, H5Gopen, H5Iget_name, H5Iget_type, H5Iis_valid, H5Lcreate_external, H5Lexists, H5Lget_info, H5Oopen, H5Oclose, H5Oget_num_attrs, H5Oget_num_attrs_by_name, H5Sclose, H5Scopy, H5Screate, H5Screate_simple, H5Sget_simple_extent_dims, H5Sis_simple, H5Sselect_index, H5Sselect_hyperslab, H5Tcopy, H5Tset_size, H5Pcreate, H5Pget_class, H5Pcopy, H5Pclose, H5Pclose_class, H5Pset_char_encoding, H5Pget_char_encoding, H5Pset_create_intermediate_group, H5Pget_create_intermediate_group, H5Pset_layout, H5Pget_layout, H5Pset_chunk, H5Pget_chunk, H5Pset_deflate, H5Pset_fill_value, H5Pfill_value_defined, H5Pset_fill_time, H5Pget_fill_time, H5Pset_alloc_time, H5Pget_alloc_time, H5Pset_chunk_cache, H5Pequal, h5const, h5constType, h5createDataset, h5createFile, h5createGroup, h5createAttribute, h5default, h5dump, h5ls, h5read, h5readAttributes, h5save, h5write, h5write.default, h5writeDataset, h5writeDataset.data.frame, h5writeDataset.list, h5writeDataset.matrix, h5writeDataset.integer, h5writeDataset.double, h5writeDataset.logical, h5writeDataset.character, h5writeDataset.array, h5writeAttribute, h5writeAttribute.matrix, h5writeAttribute.integer, h5writeAttribute.double, h5writeAttribute.logical, h5writeAttribute.character, h5writeAttribute.array, h5listIdentifier, h5validObjects, h5version ExportClasses: H5IdComponent Package: rHVDM Exports: estimerrors, fitgene, HVDMcheck, HVDMreport, screening, training, training.nl, screening.nl, fitgene.nl, fitgene.lin, .exportfree, .importfree Package: riboSeqR Exports: readRibodata, findCDS, frameCounting, readingFrame, filterHits, plotCDS, plotTranscript, sliceCounts, rnaCounts, plotFS, lengthDist ExportMethods: dim, [, show Package: Ringo Exports: autocor, chipAlongChrom1, corPlot, image, image.RGList, computeRunningMedians, sliding.quantile, findChersOnSmoothed, cherByThreshold, newCher, relateChers, preprocess, nimblegenScale, readNimblegen, asExprSet, as.data.frame.cherList, ftr2xys, compute.gc, posToProbeAnno, validProbeAnno, regionOverlap, features2Probes, sliding.meansd, computeSlidingT, getFeats, upperBoundNull, extractProbeAnno, exportCherList, plotBM, twoGaussiansNull, chipAlongChrom, quantilesOverPositions, sigGOTable, chersToBED ExportMethods: get, ls, initialize, plot, show, arrayName, chromosomeNames, genome, probes, arrayName<-, genome<-, update, cellType, cellType<-, nonzero, cbind2 ExportClasses: probeAnno, cher, qop Package: RIPSeeker Exports: addDummyProb, addPseudoAlignment, annotateRIP, binCount, combineAlignGals, computeLogOdd, computeRPKM, combineRIP, disambiguateMultihits, empiricalFDR, evalBinSize, exportGRanges, galp2gal, getAlignGal, logScoreWithControl, logScoreWithoutControl, mainSeekSingleChrom, mainSeek, nbh, nbh.GRanges, nbh.integer, nbh_chk, nbh_em, nbh_gen, nbh_init, nbh_vit, nbm_chk, nbm_em, plotCoverage, plotStrandedCoverage, randindx, ripSeek, rulebaseRIPSeek, scoreMergedBins, seekRIP, selectBinSize, statdis, viewRIP Package: Risa Exports: readISAtab, updateAssayMetadata, write.ISAtab, write.investigation.file, write.assay.file, write.study.file, getAnnotatedDataFrameAssay, getStudyFilename, getRawDataFilenames, getRawDataFilenames, getAssayRawDataFilenames, processAssayXcmsSet, processAssayXcmsSet.1factor, getMSAssayFilenames, isMSAssay, getMicroarrayAssayFilenames, isMicroarrayAssay, getMIAMEMetadata, getExpressionSet, suggestBiocPackage ExportClasses: ISATab Package: RLMM Exports: Classify, create_Thetafile, normalize_Rawfiles, plot_theta Package: Rmagpie Exports: plotErrorsRepeatedOneLayerCV, plotErrorsSummaryOneLayerCV, plotErrorsFoldTwoLayerCV ExportMethods: initialize, runOneLayerExtCV, runTwoLayerExtCV, show, getResults, getDataset, getDataset<-, getNoFolds1stLayer, getNoFolds1stLayer<-, getNoFolds2ndLayer, getNoFolds2ndLayer<-, getClassifierName, getClassifierName<-, getSvmKernel, getSvmKernel<-, getNoOfRepeats, getNoOfRepeats<-, getTypeFoldCreation, getTypeFoldCreation<-, getFeatureSelectionOptions, getFeatureSelectionOptions<-, getMaxSubsetSize, getMaxSubsetSize<-, getSubsetsSizes, getOptionValues, getOptionValues<-, getSubsetsSizes<-, getSpeed, getSpeed<-, getNoModels, getGenesFromBestToWorst, getModels, getNoThresholds, getNoThresholds<-, getFinalClassifier, rankedGenesImg, getResult1LayerCV, getResult2LayerCV, findFinalClassifier, classifyNewSamples ExportClasses: geneSubsets, assessment, finalClassifier, thresholds Package: RMassBank Exports: CTS.externalIdSubset, CTS.externalIdTypes, RmbDefaultSettings, RmbSettingsTemplate, add.formula, addMB, addPeaks, addPeaksManually, aggregateSpectra, analyzeMsMs, analyzeMsMs.formula, analyzeMsMs.intensity, annotator.default, archiveResults, cleanElnoise, combineMultiplicities, compileRecord, createMolfile, dbe, deprofile, deprofile.fwhm, deprofile.localMax, deprofile.scan, deprofile.spline, exportMassbank, filterMultiplicity, filterPeakSatellites, filterPeaksMultiplicity, findCAS, findEIC, findFormula, findMass, findMsMsHR, findMsMsHR.direct, findMsMsHR.mass, findMsMsHRperxcms.direct, findMz, findMz.formula, findName, findProgress, findRt, findSmiles, flatten, formulastring.to.list, gatherCompound, gatherData, gatherSpectrum, getCactus, getCtsKey, getCtsRecord, getMolecule, getPcId, is.valid.formula, list.to.formula, loadInfolist, loadInfolists, loadList, loadMsmsWorkspace, loadRmbSettings, loadRmbSettingsFromEnv, makeMollist, makeRecalibration, mbWorkflow, msmsRead, msmsWorkflow, multiply.formula, newMbWorkspace, newMsmsWorkspace, order.formula, parseMassBank, plotMbWorkspaces, plotRecalibration, plotRecalibration.direct, ppm, problematicPeaks, progressBarHook, readMbdata, reanalyzeFailpeak, reanalyzeFailpeaks, recalibrate, recalibrate.addMS1data, recalibrate.identity, recalibrate.linear, recalibrate.loess, recalibrate.mean, recalibrateSingleSpec, recalibrateSpectra, resetInfolists, resetList, smiles2mass, to.limits.rcdk, toMassbank, toRMB, updateSettings, validate ExportMethods: show ExportClasses: msmsWorkspace, mbWorkspace Package: rMAT ExportMethods: show, summary, rbind ExportClasses: tilingSet Package: RmiR ExportClasses: miRtcList Package: RNAinteract Exports: createCellHTSFromFiles, createRNAinteract, createRNAinteractFromFiles, getData, getMain, getMainNeg, getReplicateData, getIndDesignData, getChannelNames, getScreenNames, getScale, sgisubset, bindscreens, summarizeScreens, estimateMainEffect, normalizeMainEffectQuery, normalizeMainEffectTemplate, normalizePlateEffect, computePI, computePValues, embedPCA, plotDoublePerturbation, doublePerturbationGrob, grid.doublePerturbation, postDrawDetails.doublePerturbation, plotHeatmap, grid.sgiHeatmap, startReport, endReport, reportAnnotation, reportDoublePerturbation, reportGeneLists, reportHeatmap, reportMainEffects, reportNetworks, reportScreenData, reportStatistics ExportClasses: RNAinteract Package: RNAither Exports: createSubset, indexSubset, findReplicates, orderGeneIDs, rms, trim, closestToZero, furthestFromZero, divideChannels, eraseDataSetColumn, generateReplicateMat, generateRepMatNoFilter, summarizeReps, summarizeRepsNoFiltering, sumChannels, generateDatasetFile, joinDatasets, joinDatasetFiles, gseaAnalysis, LiWongRank, varAdjust, divNorm, quantileNormalization, BScore, ZScore, ZScorePerScreen, subtractBackground, lowessNorm, controlNorm, saveDataset, saveOldIntensityColumns, discardLabtek, discardWells, channelPlot, plotBar, ZScorePlotTwo, numCellQualControl, percCellQualControl, ZPRIMEQualControl, SNRQualControl, DRQualControl, plotControlHisto, plotControlHistoPerplate, plotControlHistoPerscreen, plotHisto, plotHistoPerplate, plotHistoPerscreen, plotQQ, plotQQperplate, plotQQperscreen, replicatesSpearmancor, replicatesCV, makeBoxplotControls, makeBoxplotControlsPerPlate, makeBoxplotControlsPerScreen, makeBoxplotPerScreen, makeBoxplotPerPlate, makeBoxplot4PlateType, spatialDistrib, compareReplicates, compareReplicaPlates, compareReplicateSD, compareReplicateSDPerScreen, controlDensity, controlDensityPerScreen, controlDensityPerPlate, ZScorePlot, Ttest, MannWhitney, RankProduct, multTestAdjust, savepValVec, incorporatepValVec, hitselectionPval, hitselectionZscore, hitselectionZscorePval, spatialDistribHits, volcanoPlot, vennDiag, compareHits, mainAnalysis, rnaither Package: RNASeqPower Exports: rnapower Package: Rnits Exports: build.Rnits, calculateGCV, fit, getCID, getFitModel, getLR, getNormTwoChannel, getPval, getStat, plotResults, summarizeProbes, timeAlign, topData ExportMethods: summary ExportClasses: Rnits Package: roar Exports: RoarDataset, RoarDatasetFromFiles ExportMethods: countPrePost, computeRoars, computePvals, computePairedPvals, totalResults, fpkmResults, countResults, standardFilter, pvalueFilter, pvalueCorrectFilter ExportClasses: RoarDataset Package: ROC Exports: AUC, AUCi, dxrule.sca, pAUC, pAUCi, ROC, rocdemo.sca, trapezint ExportMethods: plot, points, lines ExportClasses: rocc Package: Roleswitch Exports: roleswitch, getSeedMatrix, diagnosticPlot Package: rols Exports: allIds, childrenRelations, isIdObsolete, olsQuery, olsVersion, ontologies, ontologyLoadDate, ontologyNames, parents, rootId, term, termMetadata, termXrefs, as.character.Map, as.character.mapItem, as.character.CVParam, CVParam ExportMethods: key, map, value, show ExportClasses: CVParam Package: ROntoTools Exports: alpha1MR, alphaMLG, compute.fisher, compute.normalInv, keggPathwayGraphs, keggPathwayNames, pe, peEdgeRenderInfo, peNodeRenderInfo, setEdgeWeights, setNodeWeights ExportMethods: Summary, plot, nodeWeights ExportClasses: peRes, pePathway Package: RPA Exports: RPA.iteration, RPA.preprocess, collect.hyperparameters, d.update.fast, estimate.affinities, estimate.hyperparameters, frpa, get.probe.matrix, get.probe.parameters, hyperparameter.update, online.quantile, probe.parameters.tolist, probe.performance, probeplot, probetable, rpa, rpa.complete, rpa.fit, rpa.online, rpa.plot, rpa.summarize, rpaplot, sample.probeset, summarize.batch, summarize.batches, updating.hyperparameters Package: RpsiXML Exports: parsePsimi25Interaction, parsePsimi25Complex, psimi25XML2Graph, list2Matrix, complexEntry2graph, buildPCHypergraph, separateXMLDataByExpt, HPRD.PSIMI25, BIOGRID.PSIMI25, MINT.PSIMI25, INTACT.PSIMI25, DIP.PSIMI25, MIPS.PSIMI25, MATRIXDB.PSIMI25, CORUM.PSIMI25, MPACT.PSIMI25, iListHandler, eListHandler, graphConverter, hyperGraphConverter, psimi25Hypergraph2GraphNEL, bait, prey, participant, confidenceValue, inhibitor, neutralComponent, pubmedID, null2na, getAbstractByPMID, xref, complexName, attributesList, members, validatePSIMI25 ExportMethods: abstract, availableXrefs, edgeLabel, hyperedgeNodes, show, initialize, translateID, interactorInfo, interactionType, complexes, uniprot, revInciMat, releaseDate, interactors, interactions, numInteractors, numInteractions, taxId, taxId<-, organismName, organismName<-, sourceDb, sourceDb<-, sourceId, sourceId<- ExportClasses: psimi25InteractionEntry, psimi25ComplexEntry, psimi25Interactor, psimi25Interaction, psimi25Complex, psimi25Experiment, psimi25Graph, psimi25Hypergraph, psimi25Source Package: rpx Exports: PXDataset, pxannounced ExportMethods: show, pxid, pxurl, pxtax, pxref, pxfiles, pxget ExportClasses: PXDataset Package: rqubic Exports: combineBiclusts, readBiclusterResults, fcFilter, parseQubicRules, parseQubicChars, parseQubicBlocks, eSetDimName, writeQubicInputFile, quantileDiscretize, generateSeeds, quBicluster ExportMethods: BCcount, info, Svalue, RowxNumber, NumberxCol, features, featureCount, BCfeatures, BCfeatureCount, conditions, conditionCount, BCconditions, BCconditionCount, parameter ExportClasses: QUBICBiclusterSet Package: rRDP Exports: rdp, trainRDP, removeRDP, GenClass16S, encode_Greengenes, decode_Greengenes, encode_RDP, decode_RDP, accuracy, confusionTable Package: RRHO Exports: RRHO, pvalRRHO, RRHOComparison Package: Rsamtools Exports: path ExportMethods: length, names, [, [[, show, getSeq, seqinfo Package: rSFFreader Exports: availableClipModes, solveSffSEW, writePhredQual, SffReads, sread, quality, load454SampleData, loadIonSampleData, readSff, readSffGeometry, readSffHeader, SffReadsQ ExportMethods: show, detail, header, names, names<-, id, length, width, adapterClip, qualityClip, customClip, rawClip, fullClip, clipMode, adapterClip<-, qualityClip<-, customClip<-, clipMode<-, [, append, writeFasta, writeFastq, writePhredQual, writeFastaQual ExportClasses: SffHeader, SffReads, SffReadsQ Package: RSVSim ExportMethods: simulateSV, estimateSVSizes, compareSV Package: RTCA Exports: alphaNames, repairAlphaName, alphaNames2Pos, rowcol2pos, factor2numeric, relevels, parseRTCA, combineRTCA, nearestTimeIndex, sliceRTCA, ratioTransform, smoothTransform, interpolationTransform, derivativeTransform, rgrTransform, plotGridEffect, controlView, plateView, spectramaxImport ExportMethods: actionTrack, actionTrack<-, timeUnit, timeUnit<-, startTime, startTime<-, getAction, addAction, rmAction, orderAction, updateAction, reset, expID, expID<-, timeline, timeline<-, timepoints, timepoints<-, plot ExportClasses: RTCAtimeline, RTCA Package: RTN Exports: tna.plot.gsea1, tna.plot.gsea2, avs.plot1, avs.plot2 ExportMethods: tni.preprocess, tni.permutation, tni.bootstrap, tni.dpi.filter, tni.get, tni.graph, tni.conditional, tni2tna.preprocess, tna.mra, tna.gsea1, tna.gsea2, tna.overlap, tna.synergy, tna.shadow, tna.get, tna.graph, avs.preprocess, avs.vse, avs.evse, avs.get ExportClasses: TNI, TNA, AVS Package: RTopper Exports: convertToDr, computeDrStat, runBatchGSE, combineGSE, adjustPvalGSE Package: rtracklayer Exports: genomeBrowsers, start, end, strand, start<-, end<-, width, width<-, ranges, values, GenomicData, GenomicSelection, score, score<-, as.data.frame, space, ucscGenomes, BigWigSelection, GRangesForUCSCGenome, GRangesForBSGenome, summary, seqinfo, genome, genome<-, uri, Quickload, quickload, QuickloadGenome, organism, releaseDate, mcols, wigToBigWig, SeqinfoForBSGenome, SeqinfoForUCSCGenome, resource, path, FileForFormat, GFFFile, UCSCFile, BEDFile, WIGFile, ChainFile, FastaFile, GFF1File, GFF2File, GFF3File, BEDGraphFile, BED15File, GTFFile, GVFFile, BigWigFile, BigWigFileList, TwoBitFile ExportMethods: activeView, activeView<-, blocks, browseGenome, browserSession, browserSession<-, browserView, browserViews, close, export, export.bed, export.bed15, export.bedGraph, export.gff, export.gff1, export.gff2, export.gff3, export.ucsc, export.wig, export.bw, export.2bit, import, import.bed, import.bed15, import.bedGraph, import.gff, import.gff1, import.gff2, import.gff3, import.ucsc, import.wig, import.bw, import.chain, import.2bit, exportToTabix, sequence<-, track<-, track, trackNames, trackNames<-, getTable, tableNames, trackName, trackName<-, tableName, tableName<-, ucscTrackModes, ucscTrackModes<-, ucscSchema, coerce, initialize, show, summary, [, ucscTableQuery, genome, genome<-, chrom, chrom<-, range, range<-, visible, visible<-, liftOver, offset, reversed, nrow, formatDescription, referenceSequence, referenceSequence<-, asBED, asGFF, split, start, end, start<-, end<-, score, score<-, as.data.frame, space, mcols, strand, seqinfo, seqinfo<-, organism, releaseDate, getSeq ExportClasses: RTLFile, CompressedFile, GFFFile, UCSCFile, BEDFile, WIGFile, ChainFile, FastaFile, GFF1File, GFF2File, GFF3File, BEDGraphFile, BED15File, GTFFile, GVFFile, BigWigFile, BigWigFileList, TwoBitFile, BrowserSession, BrowserView, BrowserViewList, UCSCSession, UCSCView, UCSCData, TrackLine, BasicTrackLine, GraphTrackLine, Bed15TrackLine, UCSCTrackModes, BigWigSelection, UCSCSchema, Quickload, QuickloadGenome Package: Rtreemix Exports: Pval.dist, kullback.leibler, L1.dist, cosin.dist, L2.norm, euclidian.dist, rank.cor.dist, get.tree.levels, comp.models, comp.models.levels, comp.trees, comp.trees.levels, stability.sim ExportMethods: initialize, print, show, Sample, Events, Patients, Description, sampleSize, eventsNum, Events<-, Patients<-, Description<-, Weights, Weights<-, WeightsCI, Resp, CompleteMat, Star, Trees, numTrees, getTree, getData, plot, Model, LogLikelihoods, WLikelihoods, getResp, SamplingMode, SamplingParam, GPS, gpsCI, SimPatterns, SamplingTimes, WaitingTimes, getModel, noDraws, fit, bootstrap, likelihoods, gps, confIntGPS, sim, generate, distribution ExportClasses: RtreemixData, RtreemixModel, RtreemixSim, RtreemixStats, RtreemixGPS Package: RUVnormalize Exports: iterativeRUV, naiveRandRUV, naiveReplicateRUV, clScore, svdPlot Package: RUVSeq ExportMethods: RUVg, RUVs, RUVr Package: RWebServices Exports: FileReferences, urls, localNames, types, retrieve, createMap, generateDataMap, generateDataTest, generateFunctionMap, regAddonCvt, regAddonCvt2, regTestCvt, printLookup, checkJava2R, reflectObj, checkPkgVersion, getRSessionInfo, cvtCharacterFromJava, cvtCharacterToJava, matchCharacterToJava, cvtIntegerFromJava, cvtIntegerToJava, matchIntegerToJava, cvtLogicalFromJava, cvtLogicalToJava, matchLogicalToJava, cvtNumericFromJava, cvtNumericToJava, matchNumericToJava, cvtRawFromJava, cvtRawToJava, matchRawToJava, cvtComplexFromJava, cvtComplexToJava, matchComplexToJava, cvtVectorFromJava, cvtVectorToJava, matchVectorToJava, cvtListFromJava, cvtListToJava, matchListToJava, cvtArrayFromJava, cvtArrayToJava, matchArrayToJava, cvtMatrixFromJava, cvtMatrixToJava, matchMatrixToJava, cvtFactorFromJava, cvtFactorToJava, matchFactorToJava, cvtDataFrameFromJava, cvtDataFrameToJava, matchDataFrameToJava, cvtEnvFromJava, cvtEnvToJava, matchEnvToJava, cvtUnknownFromJava, cvtUnknownToJava, matchUnknownToJava, cvtFileReferencesFromJava, cvtFileReferencesToJava, matchFileReferencesToJava, cvtCharacterToJava2, matchCharacterToJava2, cvtIntegerToJava2, matchIntegerToJava2, cvtLogicalToJava2, matchLogicalToJava2, cvtNumericToJava2, matchNumericToJava2, cvtRawToJava2, matchRawToJava2, cvtComplexFromJava2, cvtComplexToJava2, matchComplexToJava2, cvtListToJava2, matchListToJava2, cvtFactorFromJava2, cvtFactorToJava2, matchFactorToJava2, cvtDataFrameFromJava2, cvtDataFrameToJava2, matchDataFrameToJava2, cvtCharArrayFromJava2, cvtCharArrayToJava2, matchCharArrayToJava2, cvtIntegerArrayFromJava2, cvtIntegerArrayToJava2, matchIntegerArrayToJava2, cvtNumericArrayFromJava2, cvtNumericArrayToJava2, matchNumericArrayToJava2, cvtLogicalArrayFromJava2, cvtLogicalArrayToJava2, matchLogicalArrayToJava2, cvtRawArrayFromJava2, cvtRawArrayToJava2, matchRawArrayToJava2, cvtComplexArrayFromJava2, cvtComplexArrayToJava2, matchComplexArrayToJava2, cvtCharMatrixFromJava2, cvtCharMatrixToJava2, matchCharMatrixToJava2, cvtIntegerMatrixFromJava2, cvtIntegerMatrixToJava2, matchIntegerMatrixToJava2, cvtNumericMatrixFromJava2, cvtNumericMatrixToJava2, matchNumericMatrixToJava2, cvtLogicalMatrixFromJava2, cvtLogicalMatrixToJava2, matchLogicalMatrixToJava2, cvtRawMatrixFromJava2, cvtRawMatrixToJava2, matchRawMatrixToJava2, cvtComplexMatrixFromJava2, cvtComplexMatrixToJava2, matchComplexMatrixToJava2, cvtEnvFromJava2, cvtEnvToJava2, matchEnvToJava2, cvtFileReferencesFromJava2, cvtFileReferencesToJava2, matchFileReferencesToJava2, unpackAntScript, sinkSetup, sinkRetrieve ExportMethods: typeInfo2Java, show, length ExportClasses: SinkOutput, RJavaSignature, RJavaPkgFunctions, FileReferences, RawMatrix, CharMatrix, LogicalMatrix, IntegerMatrix, NumericMatrix, ComplexMatrix, RawArray, CharArray, LogicalArray, IntegerArray, NumericArray, ComplexArray Package: S4Vectors Exports: aggregate.Rle, anyDuplicated.NSBS, as.data.frame.Vector, as.data.frame.Rle, as.data.frame.List, as.data.frame.DataFrame, as.list.Rle, as.list.List, as.list.SimpleList, diff.Rle, duplicated.DataTable, duplicated.Vector, duplicated.Rle, levels.Rle, mean.Rle, median.Rle, quantile.Rle, rev.Rle, sort.Vector, sort.Rle, summary.Rle, unique.DataTable, unique.Vector, unique.Rle, setValidity2, new2, setMethods, wmsg, .Call2, get_showHeadLines, get_showTailLines, printAtomicVectorInAGrid, isTRUEorFALSE, isSingleInteger, isSingleNumber, isSingleString, isSingleNumberOrNA, isSingleStringOrNA, recycleIntegerArg, recycleNumericArg, fold, safeExplode, strsplitAsListOfIntegerVectors, svn.time, normalizeSingleBracketSubscript, normalizeDoubleBracketSubscript, remapHits, List, phead, ptail, pc, SimpleList, DataFrame, isConstant, isSorted, isStrictlySorted, unstrsplit, ROWNAMES, as.env, NSBS, normalizeSingleBracketReplacementValue, extractROWS, replaceROWS, getListElement, setListElement, metadata, metadata<-, parallelSlotnames, fixedColumnNames, elementMetadata, mcols, values, elementMetadata<-, mcols<-, values<-, rename, classNameForDisplay, showAsCell, compare, selfmatch, findMatches, countMatches, queryHits, subjectHits, queryLength, subjectLength, countQueryHits, countSubjectHits, selfmatch, runLength, runLength<-, runValue, runValue<-, nrun, Rle, findRun, shiftApply, runsum, runmean, runwtsum, runq, elementType, elementLengths, isEmpty, revElements, endoapply, mendoapply ExportMethods: isConstant, isSorted, isStrictlySorted, unstrsplit, ROWNAMES, as.env, NSBS, normalizeSingleBracketReplacementValue, extractROWS, replaceROWS, getListElement, setListElement, metadata, metadata<-, fixedColumnNames, elementMetadata, mcols, values, elementMetadata<-, mcols<-, values<-, rename, classNameForDisplay, showAsCell, compare, selfmatch, findMatches, countMatches, queryHits, subjectHits, queryLength, subjectLength, countQueryHits, countSubjectHits, runLength, runLength<-, runValue, runValue<-, nrun, Rle, findRun, shiftApply, runsum, runmean, runwtsum, runq, elementType, elementLengths, isEmpty, revElements, endoapply, mendoapply, length, names, names<-, nrow, ncol, dim, NROW, NCOL, rownames, rownames<-, colnames, colnames<-, dimnames, dimnames<-, is.na, anyNA, as.logical, as.integer, as.numeric, as.complex, as.character, as.raw, as.factor, as.list, as.data.frame, as.matrix, as.table, [, [<-, subset, c, append, merge, ==, !=, <=, >=, <, >, match, duplicated, unique, anyDuplicated, %in%, sort, rank, xtfrm, t, by, transform, substr, substring, levels, levels<-, droplevels, ifelse, [[, [[<-, $, $<-, within, coerce, show, aggregate, na.omit, na.exclude, complete.cases, summary, cbind, rbind, lapply, sapply, Reduce, Filter, Find, Map, Position, unlist, do.call, xtabs, start, end, width ExportClasses: characterORNULL, vectorORfactor, DataTable, NSBS, Annotated, DataTableORNULL, Vector, Hits, Rle, List, SimpleList, DataFrame Package: sagenhaft Exports: combine.libs, compare.lib.pair, compute.sequence.neighbors, compute.unique.tags, create.matrix.csr, difference.scatter.plot, em.estimate.error.given, estimate.errors.mean, extract.ditags, extract.lib.from.directory, extract.lib.from.zip, extract.library.tags, plot.sage.library, plot.sage.library.comparison, print.sage.library, print.sage.library.comparison, read.phd.file, read.sage.library, read.sage.library.comparison, read.seq.qual.filepair, reestimate.lib.from.tagcounts, remove.sage.artifacts, revcomp, sage.test, sagelibrary.simulate, summary.sage.library, summary.sage.library.comparison, table.sparse, tagmatrix2tagnum, tagnum2tagmatrix, tagnum2tagsequence, tagsequence2tagnum, write.sage.library, write.sage.library.comparison Package: SAGx Exports: clin2mim, cluster.q, estimatep0, fetchSignal, firstpass, fom, fp.fn, Fstat, gap, GSEA.mean.t, JT.test, list.experiments, list.intersection.p, mat2TeX, myclus, normalise, one.probeset.per.gene, outlier, p0.mom, pava, pava.fdr, R2BASE, R2mim, rank.genes, rank.trend, rsd.test, samrocN, samrocNboot, union.of.pways, Xprep, Xprep.resid ExportMethods: show, plot ExportClasses: samroc.result Package: sangerseqR Exports: peakAmpMatrix<-, peakPosMatrix<-, primarySeq<-, primarySeqID<-, secondarySeq<-, secondarySeqID<-, traceMatrix<-, PolyPeakParser, chromatogram, makeBaseCalls, peakAmpMatrix, peakPosMatrix, primarySeq, primarySeqID, read.abif, read.scf, readsangerseq, sangerseq, secondarySeq, secondarySeqID, setAllelePhase, traceMatrix ExportClasses: scf, sangerseq, abif Package: SANTA Exports: BinGraph, CreateGrid, Compactness, DistGraph, GraphDiffusion, GraphMFPT, Knet, Knode, plot.Knet, SpreadHits Package: sapFinder Exports: dbCreator, runTandem, parserGear, reportCreator, easyRun Package: savR Exports: buildReports, correctedIntensities, cycles, directions, extractionMetrics, flowcellLayout, location, pfBoxplot, plotFWHM, plotIntensity, plotQGT30, qualityHeatmap, qualityMetrics, reads, run, savR, tileMetrics Package: SBMLR Exports: readSBML, readSBMLR, saveSBML, saveSBMLR, sim, S4toS3 Package: SCAN.UPC Exports: SCAN, SCANfast, UPC, UPCfast, SCAN_TwoColor, UPC_TwoColor, UPC_RNASeq, UPC_RNASeq_Single, UPC_Generic, UPC_Generic_ExpressionSet, ParseMetaFromGtfFile, InstallBrainArrayPackage, BatchAdjust, BatchAdjustFromFile Package: ScISI Exports: JaccardCoef, ScISI2html, calcGraphStats, checkComplex, checkSGN, compBijection, compareComplex, createGODataFrame, createGOMatrix, createMipsDataFrame, createMipsMatrix, createYeastDataObj, edgeProp, findSubComp, getAPMSData, getGOInfo, getLocOrfs, getMipsInfo, graphSumStats, maximizeSimilarity, meanDeg, mergeBGMat, recCompSize, rmByEvi, runAlignment, runCompareComplex, sumStats, unWantedComp, xtraGONodes ExportMethods: ID, Desc, getURL ExportClasses: yeastData Package: segmentSeq ExportMethods: dim, [, show ExportClasses: segData, alignmentData Package: SeqArray Exports: .onAttach ExportMethods: seqClose, granges, ref, alt, qual, filt, asVCF ExportClasses: SeqVarGDSClass Package: SeqGSEA Exports: DENBStat4GSEA, DENBStatPermut4GSEA, DENBTest, DEpermutePval, DSpermute4GSEA, DSpermutePval, DSresultExonTable, DSresultGeneTable, GSEAresultTable, GSEnrichAnalyze, calES, calES.perm, convertEnsembl2Symbol, convertSymbol2Ensembl, estiExonNBstat, estiGeneNBstat, exonID, exonTestability, geneID, geneList, genePermuteScore, geneScore, geneSetDescs, geneSetNames, geneSetSize, geneTestability, genpermuteMat, getGeneCount, label, loadExonCountData, loadGenesets, newGeneSets, newReadCountSet, normES, normFactor, plotES, plotGeneScore, plotSig, plotSigGeneSet, rankCombine, runDESeq, runSeqGSEA, scoreNormalization, signifES, size, subsetByGenes, topDEGenes, topDSExons, topDSGenes, topGeneSets, writeSigGeneSet, writeScores, runSeqGSEA ExportMethods: counts, counts<-, [ ExportClasses: SeqGeneSet, ReadCountSet Package: seqLogo Exports: seqLogo, makePWM ExportMethods: plot, summary, print, show ExportClasses: pwm Package: seqplots Exports: MotifSetup, getPlotSetArray, plot, plotAverage, plotHeatmap, run ExportClasses: PlotSetPair, PlotSetList, PlotSetArray, MotifSetup Package: seqTools Exports: ascii2char, countDnaKmers, countFastaKmers, countGenomeKmers, countSpliceKmers, char2ascii, kMerIndex, phredTable, fastqq, fastqKmerLocs, fastqKmerSubsetLocs, phredDist, plotPhredDist, plotPhredQuant, phredQuantiles, revCountDnaKmers, simFastqqRunTimes, sim_fq, trimFastq, writeFai, writeSimFastq, writeSimContFastq ExportMethods: cbDistMatrix, collectTime, collectDur, gcContent, gcContentMatrix, fileNames, getK, kmerCount, maxSeqLen, meltDownK, mergedPhred, mergedPhredQuantiles, mergeFastqq, nFiles, nNnucs, nReads, nucFreq, phred, plotGCcontent, plotKmerCount, plotMergedPhredQuant, plotNucCount, plotNucFreq, probeLabel, probeLabel<-, propPhred, seqLen, seqLenCount ExportClasses: Fastqq Package: SeqVarTools Exports: setVariantID ExportMethods: applyMethod, refChar, altChar, nAlleles, isVariant, isSNV, getGenotype, getGenotypeAlleles, refDosage, getVariableLengthData, titv, alleleFrequency, missingGenotypeRate, heterozygosity, homozygosity, pca, hwe, inbreedCoeff, meanBySample, mendelErr, duplicateDiscordance Package: SGSeq Exports: analyzeFeatures, analyzeVariants, annotate, convertToSGFeatures, convertToTxFeatures, exportFeatures, filterTerminalExons, findTxVariants, getBamInfo, getSGFeatureCounts, getTxVariantCounts, mergeTxFeatures, plotFeatures, plotSpliceGraph, plotVariants, predictTxFeatures, TxFeatures, SGFeatures, TxVariants, SGFeatureCounts, TxVariantCounts ExportMethods: type<-, txName<-, geneName<-, splice5p<-, splice3p<-, featureID<-, geneID<-, from<-, to<-, segmentID<-, eventID<-, variantID<-, closed5p<-, closed3p<-, variantType<-, variantName<-, featureID5p<-, featureID3p<-, counts<-, FPKM<-, countsVariant5p<-, countsVariant3p<-, countsTotal5p<-, countsTotal3p<-, variantFreq<-, type, txName, geneName, splice5p, splice3p, featureID, geneID, from, to, segmentID, eventID, variantID, closed5p, closed3p, variantType, variantName, featureID5p, featureID3p, counts, FPKM, countsVariant5p, countsVariant3p, countsTotal5p, countsTotal3p, variantFreq Package: shinyMethyl Exports: runShinyMethyl, getGreenControls, getRedControls, orderByName, shinySummarize, getPCA, shinyMethylSet ExportMethods: combine, shinySummarize, show, getBeta, getM, getMeth, getUnmeth, getCN, pData, sampleNames ExportClasses: shinyMethylSet Package: shinyTANDEM Exports: shinyTANDEM Package: ShortRead Exports: pData, phenoData, varLabels, varMetadata ExportMethods: show, coerce, dim, length, [, [[, alphabetFrequency, alphabet, coverage, encoding, narrow, reverse, reverseComplement, strand, trimLRPatterns, width, append, rbind, %in%, c, lapply, sapply Package: sigaR Exports: cghCall2cghSeg, cghCall2maximumSubset, cghCall2order, cghCall2subset, cghCall2weightedSubset, cghSeg2order, cghSeg2subset, cghSeg2weightedSubset, cisEffectPlot, cisEffectTable, cisEffectTest, cisEffectTune, CNGEheatmaps, entropyTest, expandMatching2singleIDs, ExpressionSet2order, ExpressionSet2subset, ExpressionSet2weightedSubset, getSegFeatures, hdEntropy, hdMI, matchAnn2Ann, matchCGHcall2ExpressionSet, merge2cghCalls, merge2ExpressionSets, mutInfTest, nBreakpoints, pathway1sample, pathway1sample, pathwayPlot, profilesPlot, RCMestimation, RCMrandom, RCMtest, splitMatchingAtBreakpoints, uniqGenomicInfo ExportMethods: RCMrandom, summary ExportClasses: cisTest, entTest, miTest, pathwayFit, rcmFit, rcmTest Package: SigCheck Exports: sigCheck, sigCheckClassifier, sigCheckRandom, sigCheckPermuted, sigCheckKnown, sigCheckPlot Package: SigFuge Exports: SFfigure, SFlabels, SFnormalize, SFpval Package: siggenes Exports: args.ebam, args.finda0, args.sam, ebam, ebam2excel, ebam2html, find.a0, fudge2, help.ebam, help.finda0, help.sam, link.genes, link.siggenes, list.siggenes, pi0.est, plotArguments, sam, sam2excel, sam2html, sam.plot2, d.stat, cat.stat, wilc.stat, z.ebam, cat.ebam, wilc.ebam, z.find, denspr, rowWilcoxon, rowRanksWilc, na.handling, nclass.wand, findDelta, qvalue.cal, chisqClass, chisq.ebam, chisq.stat, trend.stat, trend.ebam, md.plot, limma2sam, limma2ebam, samControl, ebamControl, fuzzy.stat, fuzzy.ebam ExportMethods: show, print, plot, summary, identify ExportClasses: SAM, EBAM, FindA0, sumSAM, sumEBAM Package: SIM Exports: assemble.data, integrated.analysis, sim.plot.pvals.on.genome, tabulate.pvals, sim.plot.pvals.on.region, sim.plot.zscore.heatmap, sim.plot.overlapping.indep.dep.features, tabulate.top.dep.features, tabulate.top.indep.features, sim.update.chrom.table, sim.plot.zoom.in, link.metadata, RESOURCERER.annotation.to.ID, impute.nas.by.surrounding, getoverlappingregions Package: SimBindProfiles Exports: eSetScatterPlot, findBoundCutoff, increasedBindingRegions, pairwiseRegions, plotBoundProbes, probeAnnoFromESet, probeLengthPlot, readSgrFiles, threewayRegions, compensationRegions Package: simpleaffy ExportMethods: [, avbg, calculated.from, calls, fc, get.array.subset, group, maxbg, means, members, minbg, pData, percent.present, plot, qc, qcProbes, ratios, sfs, spikeInProbes, target, tt ExportClasses: PairComp, QCStats Package: simulatorZ Exports: cvSubsets, funCV, geneFilter, getTrueModel, plusMinus, masomenos, simBootstrap, simData, simTime, zmatrix, rowCoxTests Package: sizepower Exports: sampleSize.randomized, sampleSize.matched, power.randomized, power.matched, power.multi Package: SLGI Exports: gi2Interactome, getInteraction, getSharedInteraction, hyperG, comemberIn, congruence, normInteraction, topInteraction, createSquareMatrix, byComplex, domainDist, getSharedDomains, sharedBy, getUniquePairs, getTestedPairs, seqMatcherAlign, getAlignStats, twoWayTable, modelSLGI, test2Interact, iSummary, withinComplex, sharedInt ExportMethods: plot, compare, show ExportClasses: siResult Package: SLqPCR Exports: geneStabM, geomMean, normPCR, relQuantPCR, selectHKgenes Package: SMAP Exports: SMAPHMM, SMAPObservations ExportMethods: name, value, noObservations, chromosome, startPosition, endPosition, reporterId, A, Pi, Phi, noStates, HMM, observations, P, Q, smap, initialize, show, plot ExportClasses: SMAPObservations, SMAPHMM, SMAPProfile, SMAPProfiles Package: SNAGEE Exports: qualStudy, qualSample, toSnageeFormat Package: snapCGH Exports: findBreakPoints, genomePlot, plotSegmentedGenome, processCGH, runBioHMM, runGLAD, runTilingArray, compareSegmentations, zoomChromosome, zoomGenome, read.clonesinfo, runHomHMM, mergeStates, runDNAcopy, simulateData, dim.SegList, length.SegList, dimnames.SegList, cbind.SegList, rbind.SegList, convert.output, filterClones, removeByWeights, find.param.five, find.param.four, find.param.three, find.param.two, find.param.one, fit.model, run.nelder, IDProbes, MergeLevels.new, MergeLevels.old, heatmapGenome, prop.na, imputeMissingValues, readPositionalInfo, generate.data, Viterbi.five, Viterbi.four, Viterbi.three, Viterbi.two, log2ratios ExportClasses: SegList Package: snm Exports: snm, sim.singleChannel, sim.doubleChannel, sim.preProcessed, sim.refDesign Package: SNPchip Exports: plotCytoband, plotIdiogram, xypanel, arrangeSideBySide, centromere, xyplotLrrBaf, xypanelBaf, plotCytoband2, getCytoband, latticeFigs, arrangeFigs ExportMethods: dataFrame, xyplot2 Package: SNPRelate Exports: .onAttach Package: snpStats Exports: can.impute, convert.snpMatrix, convert.snpMatrix.dir, filter.rules, Fst, glm.test.control, g2post, ibsCount, ibsDist, impute.snps, imputation.maf, imputation.r2, imputation.nsnp, ld, mean2g, misinherits, mvtests, plotUncertainty, pool, post2g, pp, qq.chisq, read.beagle, read.impute, read.long, read.mach, read.pedfile, read.plink, read.snps.long, row.summary, col.summary, single.snp.tests, sm.compare, snp.cor, snp.imputation, snp.lhs.tests, snp.lhs.estimates, snp.post.multiply, snp.pre.multiply, snp.rhs.tests, snp.rhs.estimates, tdt.snp, test.allele.switch, write.plink, write.SnpMatrix, xxt ExportMethods: cbind, chi.squared, deg.freedom, effect.sign, is.na, names, pool2, p.value, rbind, show, summary, switch.alleles, plot, sample.size, effective.sample.size, [, [<-, coerce, initialize ExportClasses: SnpMatrix, XSnpMatrix, ImputationRules, SingleSnpTests, SingleSnpTestsScore, GlmTests, GlmEstimates Package: SomatiCA ExportMethods: SomatiCAFormat Package: SomaticSignatures Exports: readMutect, ucsc, ncbi, seqchar, mutationContext, mutationContextMutect, mutationContextH5vc, kmerFrequency, mutationDistance, plotRainfall, plotVariantAbundance, motifMatrix, identifySignatures, plotMutationSpectrum, plotObservedSpectrum, plotFittedSpectrum, plotSignatureMap, plotSignatures, plotSampleMap, plotSamples, gcContent, hsToplevel, hsAutosomes, hsAllosomes, hsLinear, normalizeMotifs, clusterSpectrum, nmfDecomposition, pcaDecomposition, nmfSignatures, pcaSignatures, scaSNVRanges ExportMethods: show, signatures, samples, observed, fitted ExportClasses: MutationalSignatures Package: SpacePAC Exports: SpaceClust, make.3D.Sphere Package: spade Exports: SPADE.addDensityToFCS, SPADE.transform.FCS, SPADE.downsampleFCS, SPADE.FCSToTree, SPADE.addClusterToFCS, SPADE.annotateMarkers, SPADE.markerMedians, SPADE.layout.arch, SPADE.write.graph, SPADE.annotateGraph, SPADE.driver, SPADE.density, SPADE.plot.trees, SPADE.flattenAnnotations, SPADE.installPlugin, SPADE.read.FCS, SPADE.removeExistingDensityAndClusterColumns Package: specL Exports: read.bibliospec, annotateProteinID, genSwathIonLib ExportMethods: show, plot, write.Spectronaut, ionlibrary, rt.input, rt.normalized ExportClasses: specL, specLSet Package: SpeCond Exports: getDefaultParameter, createParameterMatrix, fitPrior, fitNoPriorWithExclusion, getSpecificResult, getSpecificOutliersStep1, SpeCond, getMatrixFromExpressionSet, getProfile, writeSpeCondResult, writeUniqueProfileSpecificResult, writeGeneResult, getFullHtmlSpeCondResult, getGeneHtmlPage Package: SPEM Exports: SPEM, row_optimize, s_diff Package: SPIA Exports: spia, plotP, combfunc, makeSPIAdata Package: spikeLI Exports: collapse, Ivsc, IvsDG Package: spkTools Exports: plotSpkBox, spkAccSD, spkAll, spkAnova, spkBal, spkBox, spkDensity, spkGNN, spkMA, spkPair, spkPairNS, spkPot, spkQuantile, spkSlope, spkVar, summarySpkBox ExportMethods: initialize, spikeIn, spkSplit ExportClasses: SpikeInExpressionSet Package: spliceR ExportClasses: CDSSet, SpliceRList Package: spliceSites Exports: alignGapList, as.data.frame.gapSites, countByGeneName, dnaGapSites, gapSites, load.hbond, load.maxEnt, silic_tryp, rangeByGeneName, readCuffGeneFpkm, readExpSet, readMergedBamGaps, readTabledBamGaps, getGapSites, merge.gapSites, truncate_seq ExportMethods: addHbond, addKeyTable, addGeneAlignPart, addMaxEnt, basedir, basedir<-, appendKeyTable, alt_ranks, annotate, annotation, annotation<-, dnaRanges, alt_left_ranks, alt_right_ranks, c, count, dim, dnaGapSites, end, extractByGeneName, extractRange, getAnnStrand, getKeyTable, getMeStrand, getProfile, getSequence, gptm, hbond, head, id, initialize, lCodons, lend, lJunc, lJuncStrand, lrCodons, lrJunc, lrJuncStrand, lstart, nAligns, nAlignGaps, plot_diff, plot_diff_ranks, rCodons, rend, resize_left, resize_right, rJunc, rJuncStrand, rpmg, rstart, saveMaxEnt, score3, score5, scoreSeq5, scoreSeq3, seqid, seqlogo, setMeStrand, show, sortTable, start, strand, strand<-, translate, trim_left, trim_right, truncateSeq, trypsinCleave, uniqueJuncAnn, width, write.annDNA.tables, write.files ExportClasses: annGapSites, aaGapSites, caRanges, cdRanges, cRanges, dnaGapSites, gapSites, hbond, maxEnt Package: SplicingGraphs Exports: slideshow, rsgedges, sgedges2, rsgraph, sgraph2, ASCODE2DESC, assignReads, removeReads, toy_genes_gff, toy_reads_sam, toy_reads_bam, toy_overlaps, SplicingGraphs, plotTranscripts, sgedgesByTranscript, sgedgesByGene, txpath, txweight, txweight<-, sgedges, sgnodes, outdeg, indeg, sgraph, uninformativeSSids, rsgedgesByTranscript, rsgedgesByGene, bubbles, reportReads, countReads ExportMethods: SplicingGraphs, plotTranscripts, sgedgesByTranscript, sgedgesByGene, txpath, txweight, txweight<-, sgedges, sgnodes, outdeg, indeg, sgraph, uninformativeSSids, rsgedgesByTranscript, rsgedgesByGene, bubbles, reportReads, countReads, length, names, show, [, [[, elementLengths, unlist, seqnames, strand, seqinfo, intronsByTranscript, plot ExportClasses: GeneModel, SplicingGraphs Package: splots Exports: plotScreen Package: spotSegmentation Exports: spotseg, spotgrid, plotBlockImage Package: SQUADD Exports: simResService ExportMethods: [, [<-, getFittedTable, plotCC, plotPredMap, plotSimMatrix ExportClasses: SquadSimResServiceImpl Package: sRAP Exports: RNA.norm, RNA.qc, RNA.deg, RNA.bdfunc.fc, RNA.bdfunc.signal Package: sscore Exports: computeAffxSFandSDT, computeSFandSDT, SScore, SScoreBatch Package: ssize Exports: delta, delta.plot, pow, power.plot, power.t.test.FDR, ssize, ssize.plot Package: SSPA Exports: dbitri, pbitri, pilotData, predictpower, qbitri, rbitri, sampleSize, simdat ExportMethods: plot Package: ssviz ExportMethods: plotPP, plotDistro, plotFreq, plotRegion, readBam, pingpong, ntfreq, getCountMatrix ExportClasses: logicalORmissing Package: STAN Exports: HMM, HMMEmission, bdHMM, getViterbi, fitHMM, getPosterior ExportClasses: bdHMM, HMMEmission, HMM Package: staRank Exports: RankSummary, aggregRank, dataFormatRSA, getRankmatrix, getStability, mwTest2samp, runRSA, uniqueRSARanking ExportMethods: summaryStats, stableSetSize, stabilityRanking, stabRank, rankCor, method, getSampleScores, baseRank, avrgRank, Pi ExportClasses: RankSummary Package: Starr Exports: bpmapToProbeAnno, profileplot, correlate, correlationPlot, expressionByFeature, fill, fillNA, filterGenes, getFeature, getIntensities, getMeans, getProfiles, getProfilesByBase, getRatio, intersection, list2matrix, makeProbeAnno, mapFeatures, normalize.Probes, plotBoxes, plotDensity, plotGCbias, plotImage, plotMA, plotPosBias, plotProfiles, rankPercentile.normalize, read.gffAnno, readCelFile, RGlist2ExpresionSet, sameLength, singleclusterplot, substract, whichIn, windowxy, writeGFF, writePosFile, densityscatter, kde2dplot, plotScatter, plotRatioScatter, makeSplines, backgd.sd, cmarrt.ma, cmarrt.peak, declare.bound, ma.stat, plotcmarrt, rm.small.peak, sortbygenomic, remap, match_ac, heatmapplot, writeWIG Package: STATegRa Exports: bioMap, bioDistclass, bioDistFeaturePlot, STATegRaUsersGuide ExportMethods: getPreprocessing, getScores, getMethodInfo, getLoadings, getVAF, getInitialData, biplotRes, plotRes, plotVAF, omicsCompAnalysis, PCA.selection, modelSelection, selectCommonComps, bioDistFeature, bioDistWPlot, bioDistW, bioDist, createOmicsExpressionSet ExportClasses: bioDistclass, bioMap Package: stepNorm Exports: aov2Dfit, calcAIC, calcBIC, calcEnp, fit2DWithin, fitWithin, loess2Dfit, loessfit, maCompPlate2, makeStepList, medfit, MedianSmooth, noFit, rlm2Dfit, rlmfit, seqWithinNorm, spatialMedfit, square, stepWithinNorm, withinNorm ExportClasses: marrayFit Package: Streamer ExportMethods: lapply, sapply ExportClasses: Streamer, Stream, Producer, RawInput, Seq, FunctionProducer, ConnectionProducer, Consumer, RawToChar, Rev, Downsample, Reducer, FunctionConsumer, Team, ParallelParam, MulticoreParam, DAGTeam, DAGParam Package: STRINGdb Exports: STRINGdb, coeffOfvar, delColDf, downloadAbsentFile, downloadAbsentFileSTRING, get_STRING_species, multi_map_df, plot_ppi_enrichment_graph, ppi_enrichment, ppi_enrichment_full, ppie.compLambda, ppie.compLambdaL1L2, ppie.compPij, ppie.getNumEdgesBetween, renameColDf ExportClasses: STRINGdb Package: supraHex Exports: sBMH, sCompReorder, sDistance, sDmat, sDmatCluster, sDmatMinima, sHexDist, sHexGrid, sInitial, sMapOverlay, sNeighAny, sNeighDirect, sPipeline, sTopology, sTrainBatch, sTrainSeq, sTrainology, sWriteData, visColoralpha, visColorbar, visColormap, visCompReorder, visDmatCluster, visDmatHeatmap, visHeatmap, visHeatmapAdv, visHexComp, visHexGrid, visHexMapping, visHexMulComp, visHexPattern, visKernels, visTreeBootstrap, visVp Package: Sushi Exports: addlegend, labelgenome, labelplot, maptocolors, maptolwd, opaque, plotBed, plotBedgraph, plotBedpe, plotGenes, plotHic, plotManhattan, SushiColors, zoombox, zoomsregion Package: sva Exports: ComBat, empirical.controls, f.pvalue, fstats, fsva, irwsva.build, num.sv, psva, ssva, sva, sva.check, svaseq, twostepsva.build Package: SwimR Exports: createFrequencyMatrix, SwimR Package: switchBox Exports: SWAP.CalculateSignedScore, SWAP.KTSP.Train, SWAP.KTSP.Statistics, SWAP.KTSP.Classify, SWAP.Filter.Wilcoxon, KTSP.Train, KTSP.Classify Package: synapter Exports: Synapter, as.MSnSet.Synapter, synergise, synapterGUI, makeMaster, writeMasterPeptides, estimateMasterFdr, inspectPeptideScores, synapterGuide, synapterTinyData ExportMethods: show, inputFiles, getLog, mergePeptides, modelRt, findEMRTs, searchGrid, getGrid, getGridDetails, getBestGridValue, getBestGridParams, setBestGridParams, setPepScoreFdr, getPepScoreFdr, setProtFpr, getProtFpr, setIdentPpmError, getIdentPpmError, setQuantPpmError, getQuantPpmError, setPpmError, setLowessSpan, getLowessSpan, setRtNsd, getRtNsd, getPpmErrorQs, getRtQs, getPepNumbers, showFdrStats, getEMRTtable, performance, performance2, filterPeptideLength, filterQuantPepScore, filterIdentPepScore, filterIdentPpmError, filterQuantPpmError, filterIdentProtFpr, filterQuantProtFpr, filterUniqueDbPeptides, filterUniqueQuantDbPeptides, filterUniqueIdentDbPeptides, plotPpmError, plotRtDiffs, plotRt, plotPepScores, plotFdr, plotEMRTtable, plotGrid, plotFeatures, writeMergedPeptides, writeMatchedEMRTs, writeIdentPeptides, writeQuantPeptides, bestComb, allComb, masterFdr, fileNames, plot ExportClasses: MasterPeptides, MasterFdrResults Package: systemPipeR Exports: readComp, writeTargetsout, alignStats, getQsubargs, qsubRun, clusterRun, returnRPKM, runCommandline, systemArgs, symLink2bam, moduleload, modulelist, run_edgeR, run_DESeq2, filterDEGs, seeFastq, seeFastqPlot, GOHyperGAll, GOHyperGAll_Subset, GOHyperGAll_Simplify, GOCluster_Report, makeCATdb, goBarplot, overLapper, vennPlot, olBarplot, preprocessReads ExportMethods: targetsin, targetsout, targetsheader, modules, software, cores, other, reference, results, infile1, infile2, outfile1, SampleName, sysargs, outpaths, show, names, length, [, catmap, catlist, idconv, setlist, intersectmatrix, complexitylevels, vennlist, intersectlist, as.list ExportClasses: SYSargs, catDB, VENNset, INTERSECTset Package: TargetScore Exports: bsxfun.se, dot.ext, getTargetScores, initialization, logmvgamma, logsumexp, sort_components, targetScore, vbgmm, vbound, vexp, vmax Package: TargetSearch Exports: FAMEoutliers, FindPeaks, medianRILib, Profile, sampleRI, ImportLibrary, ImportLibrary.tab, ImportLibrary.msp, ImportSamples, ImportSamplesFromDir, ImportFameSettings, NetCDFPeakFinding, peakCDFextraction, peakFind, plotFAME, plotRIdev, plotAllRIdev, plotPeakSimple, plotPeak, plotSpectra, plotAllSpectra, quantMatrix, ProfileCleanUp, RIcorrect, rt2ri, ri2rt, Write.Results, writeMSP, baseline, baselineCorrection, fixRIcorrection, TargetSearchGUI, writeLibText, bin2text, text2bin, riMatrix, fixRI ExportMethods: rimMass, rimMass<-, rimLimits, rimLimits<-, rimStandard, rimStandard<-, CDFfiles, CDFfiles<-, RIfiles, RIfiles<-, CDFpath, CDFpath<-, RIpath, RIpath<-, sampleData, sampleData<-, sampleNames, sampleNames<-, sampleDays, sampleDays<-, refLib, libId, medRI, medRI<-, selMass, selMass<-, topMass, topMass<-, quantMass, quantMass<-, spectra, spectra<-, libName, libName<-, libRI, libRI<-, libData, libData<-, RIdev, RIdev<-, retIndex, retIndex<-, retTime, retTime<-, Intensity, Intensity<-, as.list.tsMSdata, as.list.tsProfile, profileInfo, profileInfo<-, profileInt, profileInt<-, profileRI, profileRI<-, profileRT, profileRT<-, fileFormat, fileFormat<-, show ExportClasses: tsLib, tsRim, tsSample, tsMSdata, tsProfile Package: TCC Exports: show.TCC, names, length, [, TCC, calcAUCValue, calcNormFactors, estimateDE, filterLowCountGenes, simulateReadCounts, getNormalizedData, getResult, plotFCPseudocolor, plot.TCC, WAD, ROKU, clusterSample ExportClasses: TCC Package: TDARACNE Exports: TDARACNEdataPublished, TDARACNE Package: TEQC Exports: chrom.barplot, coverage.correlation, coverage.density, coverage.hist, coverage.GC, coverage.plot, coverage.target, coverage.targetlength.plot, coverage.uniformity, covered.k, duplicates.barplot, fraction.reads.target, fraction.target, get.baits, get.reads, get.targets, insert.size.hist, make.wigfiles, multiTEQCreport, reads2pairs, readsPerTarget, TEQCreport Package: ternarynet Exports: tnetfit, tnetpost, ternaryFit, ternaryFitParameters, ternaryPost, graphPosterior, attractorSummary, plotTraces, plotFit, plotPost, predictAttractor, simulateSteadyState ExportMethods: scores, degreeObjs, graphObjs, tableObjs, scores<-, degreeObjs<-, graphObjs<-, tableObjs<-, perturbationType, scoreType, backupStage, maxStage, maxTransition, epsilon, beta0, chi0, delta, ne, m0, maxDegree, pAddParent, pExchangeParent, neighborDegree, pNeighborhood, rho, edgePenalty, show, perturbationType<-, scoreType<-, backupStage<-, maxStage<-, maxTransition<-, epsilon<-, beta0<-, chi0<-, delta<-, ne<-, m0<-, maxDegree<-, pAddParent<-, pExchangeParent<-, neighborDegree<-, pNeighborhood<-, rho<-, edgePenalty<-, dim, perturbationObj, steadyStateObj, geneNames, experimentNames, degreeObjMin, graphObjMin, tableObjMin, newScore, minScore, finalTemperature, traces, stageCount, xSeed, inputParams, perturbationObj<-, steadyStateObj<-, geneNames<-, experimentNames<-, degreeObjMin<-, graphObjMin<-, tableObjMin<-, newScore<-, minScore<-, finalTemperature<-, traces<-, stageCount<-, xSeed<-, inputParams<- ExportClasses: ternaryFitParameters, ternaryFit, ternaryPost Package: TFBSTools Exports: PFMatrix, PFMatrixList, ICMatrix, ICMatrixList, PWMatrix, PWMatrixList, MotifSet, SitePairSetList, SitePairSet, SiteSet, SiteSetList, shannon.entropy, storeMatrix, getMatrixSet, getMatrixByID, getMatrixByName, deleteMatrixHavingID, initializeJASPARDB, ID, name, matrixClass, Matrix, Matrix<-, bg, tags, matrixType, XMatrixList, colSums, rowSums, toPWM, searchSeq, searchAln, searchPairBSgenome, PWMSimilarity, toICM, seqLogo, totalIC, writeGFF3, writeGFF2, relScore, views, pvalues, toGRangesList, calConservation, PFMSimilarity, permuteMatrix, dmmEM, rPWMDmm, runMEME, sitesSeq ExportMethods: length, ncol, dim, reverseComplement, as.matrix, consensusMatrix ExportClasses: PFMatrix, PWMatrix, ICMatrix, PFMatrixList, PWMatrixList, ICMatrixList, SiteSet, SiteSetList, SitePairSet, SitePairSetList, MotifSet Package: tilingArray Exports: normalizeByReference, segment, costMatrix, findSegments, sampleStep, readCel2eSet, posMin, otherStrand, plotAlongChrom, plotAlongChromLegend, plotSegmentationHeatmap, plotSegmentationDots, plotFeatures, comparisonPlot, plotPenLL, qcPlots, PMindex, BGindex, segChrom, residuals.breakpointsPretend, breakpoints.breakpointsPretend ExportMethods: plot, show, confint, logLik ExportClasses: segmentation Package: timecourse Exports: abs2ratio, matrix.cov, mb.1D, mb.2D, mb.long, mb.MANOVA, mb.paired, ot.helmert, plotProfile, univ.func ExportClasses: MArrayTC, LargeDataObject Package: TitanCNA Exports: loadAlleleCounts, loadDefaultParameters, extractAlleleReadCounts, filterData, getPositionOverlap, wigToRangedData, outputTitanResults, outputModelParameters, correctReadDepth, runEMclonalCN, viterbiClonalCN, computeSDbwIndex, plotAllelicRatio, plotClonalFrequency, plotCNlogRByChr, plotSubcloneProfiles Package: tkWidgets Exports: DPExplorer, args2XML, argsWidget, dataViewer, dbArgsWidget, eExplorer, fileBrowser, fileWizard, find.type, guess.header, guess.sep, importPhenoData, importWizard, listSelect, objViewer, objectBrowser, pExplorer, pickItems, tkMIAME, tkSampleNames, tkphenoData, vExplorer, viewVignette, WLValue<-, WName, WRButtons, values.Widget, WValue, WValue<-, WbuttonFun, WbuttonText, WcanEdit, WfromText, WpostFun, WpreFun, WtoText, WwList, WwList<-, print.Widget, WLValue, WEnd, appendSepDir, getWvalues, hasChar, stdType, objNameToList, getPkgContents, getFileContents, pickFiles, pickObjs, print.pWidget, hasPrefix, hasSuffix, hasChar, formatArg ExportClasses: colInfo Package: ToPASeq Exports: SPIA, DEGraph, Clipper, TBS, PWEA, TAPPA, TopologyGSA, res, topo.sig, degtable, convertIdentifiersByVector, AdjacencyMatrix2Pathway, graphNEL2Pathway, reduceGraph Package: topGO Exports: annFUN.db, annFUN, annFUN.gene2GO, annFUN.GO2genes, annFUN.org, annFUN.file, combineResults, readMappings, inverseList, whichAlgorithms, whichTests, GOplot, showSigOfNodes, getPvalues, showGroupDensity, reverseArch, nodesInInducedGraph, inducedGraph, buildLevels, getNoOfLevels, getGraphRoot, permSumStats, permSumStats.all, groupGOTerms, .genesInNode, .countsInNode ExportMethods: initialize, description, ontology, allGenes, feasible, graph, geneSelectionFun, description<-, ontology<-, feasible<-, graph<-, geneSelectionFun<-, print, show, updateGenes, genes, numGenes, geneScore, sigGenes, numSigGenes, usedGO, attrInTerm, genesInTerm, scoresInTerm, countGenesInTerm, termStat, updateTerm<-, allMembers, Name, members, testStatistic, Name<-, allMembers<-, members<-, numMembers, numAllMembers, runTest, sigMembers<-, sigAllMembers, numSigAll, sigMembers, numSigMembers, contTable, allScore, membersScore, score<-, rankMembers, pType, pType<-, membersExpr, getSigGroups, elim, cutOff, elim<-, cutOff<-, updateGroup, Weights<-, Weights, sigRatio<-, getSigRatio, score, testName, algorithm, geneData, geneData<-, testName<-, algorithm<-, printGenes, penalise, scoreOrder, testStatPar, printGraph, GenTable, GOFisherTest, GOKSTest, GOtTest, GOglobalTest, GOSumTest, GOKSTiesTest, joinFun, allParents, depth, depth<-, expressionMatrix, phenotype ExportClasses: topGOdata, topGOresult, groupStats, classicCount, classicScore, classicExpr, weight01Count, weight01Score, weight01Expr, elimCount, elimScore, elimExpr, leaCount, leaScore, leaExpr, weightCount, pC, parentChild Package: tracktables Exports: MakeIGVSampleMetadata, MakeIGVSession, MakeIGVSessionXML, igvParam, makebedtable, maketracktable Package: trackViewer Exports: addArrowMark, addGuideLine, coverageGR, geneModelFromTxdb, getCurTrackViewport, importBam, importScore, interactiveViewer, optimizeStyle, trackList, trackViewerStyle, viewTracks ExportMethods: setTrackViewerStyleParam, setTrackStyleParam, setTrackXscaleParam, setTrackYaxisParam, $, $<- ExportClasses: pos, trackStyle, trackViewerStyle, track, trackList, xscale, yaxisStyle Package: tRanslatome Exports: newTranslatomeDataset, computeDEGs, getExprMatrix, getConditionA, getConditionB, getConditionC, getConditionD, getDataType, getConditionLabels, getLevelLabels, getDEGs, Histogram, Scatterplot, MAplot, SDplot, CVplot, GOEnrichment, RegulatoryEnrichment, DEGs.table, getDEGsMethod, significance.threshold, FC.threshold, label.level.DEGs, label.condition, Radar, Heatmap, enriched.table, label.level.enriched, GOComparison, IdentityPlot, SimilarityPlot, identity.matrix, similarity.matrix, average.similarity.scores Package: TransView Exports: plotTV, parseReads, rmTV, annotatePeaks, gtf2gr, macs2gr, peak2tss, meltPeak ExportMethods: show, sliceN, slice1, sliceNT, slice1T, tvStats, plotTVData, histogram, ex_name, origin, spliced, paired, readthrough_pairs, filtered, strands, nreads, gcoverage, maxScore, lowqual, paired_reads, proper_pairs, collapsed, compression, chromosomes, filtered_reads, pos, neg, lcoverage, lmaxScore, fmapmass, env, data_pointer, spliced<-, ex_name<-, size, parameters, cluster_order, clusters, summaryTV, lsize, gsize ExportClasses: DensityContainer Package: triform Exports: preprocess, triform Package: trigger Exports: trigger.build ExportMethods: trigger.link, trigger.mlink, trigger.eigenR2, trigger.loclink, trigger.net, trigger.netPlot2ps, trigger.export2cross, trigger.trait, plot ExportClasses: trigger Package: trio Exports: trio.sim, trio.prepare, trio.check, getLD, findLDblocks, splitBlocks, tdt, colTDT, tdt2way, colTDT2way, colTDTinter2way, compPermTDT2way, ped2geno, read.pedfile, removeSNPs, removeTrios, orderSNPs, colMAFtrio, colTDTmaxStat, colTDTmaxTest, colGxE, colGxEPerms, trio.permTest, colTDTsam, colTDTebam, gtdt.stat, gtdt.ebam, fastGxG, fastGxGrec, poly4root, poly4rootMat, scoreTDT, scoreGxE, scoreMaxStat, scoreGxG, trioLR, trioFS, lrControl, getMatPseudo, getGxEstats, colGxG, tdtGxG, colGxGPerms, allelicTDT, getLDlarge, trio.power, probTDT, colPOlrt, colTAT, vcf2geno, colEMlrt Package: triplex Exports: triplex.search, triplex.diagram, triplex.3D, triplex.alignment, triplex.score.table, triplex.group.table ExportMethods: show, score, pvalue, ins, type, lstart, lwidth, lend, strand, as.character, toString ExportClasses: TriplexViews Package: TSCAN Exports: TSCANui, TSPpseudotime, difftest, orderscore, plotpseudotime, preprocess, singlegeneplot Package: tspair Exports: ts.pair, tspcalc, tspsig, tspplot Package: TSSi Exports: subtractExpectation, assessPoisson, assessGradPoisson ExportMethods: plot, readsAsRangedData, segmentsAsRangedData, tssAsRangedData, show, names, start, end, counts, ratio, fit, expect, reads, segments, tss, parameters, annotation, [, identifyStartSites, normalizeCounts, segmentizeCounts ExportClasses: TssResult, TssNorm, TssData Package: TurboNorm Exports: pspline, normalize.pspline, normalize.AffyBatch.pspline, turbotrend, panel.pspline Package: tweeDEseq Exports: compareCountDist, testPoissonTweedie, mlePoissonTweedie, dPT, rPT, testShapePT, getParam, normalizeCounts, filterCounts, tweeDE, gofTest, qqchisq, MAplot, Vplot, glmPT, tweeDEglm, exactTestPT, tweeDExact Package: twilight Exports: plot.twilight, print.twilight, twilight, twilight.combi, twilight.filtering, twilight.getlambda, twilight.getmatrix, twilight.permute.pair, twilight.permute.unpair, twilight.pval, twilight.teststat Package: TypeInfo Exports: IndependentTypeSpecification, SimultaneousTypeSpecification, ReturnTypeSpecification, TypedSignature, StrictIsTypeTest, InheritsTypeTest, checkArgs, checkReturnValue, typeInfo, typeInfo<-, paramNames, hasParameterType, hasReturnType ExportMethods: initialize, coerce, checkArgs, showTypeInfo ExportClasses: TypedSignature, NamedTypeTest, InheritsTypeTest, StrictIsTypeTest, DynamicTypeTest, ClassNameOrExpression, TypeSpecification, IndependentTypeSpecification, SimultaneousTypeSpecification, ReturnTypeSpecification Package: unifiedWMWqPCR Exports: as.matrix, coef, esttype, forestplot, getEstimate, getOrder, groupinfo, housekeeping, is.unsorted, logor, oddsRatio, orderedBy, plot, pval, ref, se, type, uWMW, unorder, vcov, volcanoplot, zval ExportMethods: vcov, unorder, sort, plot, names, esttype, coef, [ ExportClasses: uwmwRes, uwmwEstimate Package: UniProt.ws Exports: columns, availableUniprotSpecies, lookupUniprotSpeciesFromTaxId ExportMethods: keytypes, columns, keys, select, taxId, taxId<-, species Package: VanillaICE Exports: baf_means<-, baf_sds<-, cn_means<-, cn_sds<-, emission<-, emissionParam<-, ArrayViews, BeadStudioSet, BeadStudioSetList, CopyNumScanParams, EMupdates, EmissionParam, FilterParam, HMM, HMMList, HmmOptionList, HmmParam, HmmTrellisParam, IdiogramParams, LogLik, NA_filter, SnpArrayExperiment, SnpExperiment, SnpGRanges, TransitionParam, bafFile, baf_means, baf_sds, baumWelchUpdate, calculateEmission, cn_means, cn_sds, cnvFilter, cnvSegs, colModes, constrainMu2, constrainSd2, copyNumberLimits, deletion, doUpdate, dropDuplicatedMapLocs, dropSexChrom, duplication, emission, emissionParam, fileName, filters, getExampleSnpExperiment, getHmmParams, gtFile, hemizygous, hmm, hmm2, homozygous, icePlatforms, lrrFile, numberFeatures, parseSourceFile, parsedPath, probability, read.bsfiles, rescale, robustSds, rowMAD, rowModes, segs, snpArrayAssays, sourcePaths, sweepMode, threshold, updateHmmParams, viewports, viterbi2Wrapper, xygrid, xyplotList ExportMethods: state, start, show, sapply, plot, nrow, ncol, lrr, length, genotypes, dim, copyNumber, baf, colnames<-, [[ ExportClasses: SnpGRanges, SnpArrayExperiment, LogLik, IdiogramParams, HMMList, HMM, FilterParam, CopyNumScanParams, ArrayViews Package: VariantAnnotation Exports: VCF, VCFHeader, reference, header, header<-, meta, meta<-, vcfWhich, vcfWhich<-, vcfFixed, vcfFixed<-, vcfInfo, vcfInfo<-, vcfGeno, vcfGeno<-, vcfSamples, vcfSamples<-, vcfTrimEmpty, vcfTrimEmpty<-, duplicateRSID, CodingVariants, IntronVariants, FiveUTRVariants, ThreeUTRVariants, IntergenicVariants, SpliceSiteVariants, PromoterVariants, AllVariants, upstream, upstream<-, downstream, downstream<-, promoter, promoter<-, intergenic, intergenic<-, probabilityToSnpMatrix, GLtoGP, restrictToSNV, VRanges, VRangesList, asVCF, softFilter, resetFilter, totalDepth, altDepth, refDepth, sampleNames, sampleNames<-, altFraction, softFilterMatrix, softFilterMatrix<-, hardFilters, hardFilters<-, called, stackSamples, altDepth<-, refDepth<-, totalDepth<-, probabilityToSnpMatrix, GLtoGP, readInfo, readGeno, readGT, tabulate, VRangesScanVcfParam, readVcfAsVRanges, isSNV, isInsertion, isDeletion, isIndel, isTransition, isSubstitution ExportMethods: filterVcf, scanVcf, scanVcfHeader, ScanVcfParam, readVcf, writeVcf, expand, readVcfLongForm, predictCoding, getTranscriptSeqs, refLocsToLocalLocs, genotypeToSnpMatrix, snpSummary, locateVariants, summarizeVariants, isSNV, isInsertion, isDeletion, isIndel, isTransition, isSubstitution, fixed, fixed<-, ref, ref<-, alt, alt<-, qual, qual<-, filt, filt<-, info, info<-, geno, geno<-, strand, strand<-, [, [<-, cbind, rbind, mcols<-, genome, seqlevels, seqinfo, reference, samples, header, meta, keys, keytypes, columns, select Package: VariantFiltering Exports: reportVariants, readWm, readAAradicalChangeMatrix, codeAF2RAW, decodeRAW2AF, PhastConsDb, GenePhylostrataDb ExportMethods: VariantFilteringParam, annotateVariants, width, conservedPositions, show, xLinked, autosomalRecessiveHomozygous, autosomalDominant, deNovo, autosomalRecessiveHeterozygous, unrelatedIndividuals, allInheritanceModels, wmScore, inheritanceModel, param, allVariants, filteredVariants, selectIndividual, selectIndividual<-, dbSNPpresent, dbSNPpresent<-, OMIMpresent, OMIMpresent<-, variantType, variantType<-, aaChangeType, aaChangeType<-, MAFpop, MAFpop<-, naMAF, naMAF<-, maxMAF, maxMAF<-, minPhastCons, minPhastCons<-, minPhylostratum, minPhylostratum<-, minCRYP5ss, minCRYP5ss<-, minCRYP3ss, minCRYP3ss<-, knownVariantsMAFcols, fetchKnownVariantsByID, keytypes, keys, columns, select, provider, providerVersion, referenceGenome, organism, seqinfo, seqnames, seqlengths, scores, genePhylostratum, genePhylostrata ExportClasses: MafDb, PhastConsDb, GenePhylostrataDb, VariantFilteringParam, VariantFilteringResults, VariantFilteringResultsUI, VariantFilteringResultsAIM, WeightMatrix Package: VariantTools Exports: callVariants, qaVariants, tallyVariants, postFilterVariants, calculateConcordanceMatrix, callVariantConcordance, calculateVariantConcordance, VariantQAFilters, VariantCallingFilters, VariantTallyParam, VariantPostFilters, TallyVariantsParam, variantGR2Vcf, callSampleSpecificVariants, SampleSpecificVariantFilters, callWildtype, minCallableCoverage, matchVariants, %variant_in%, extractCoverageForPositions, pileupVariants, makeVRangesFromVariantGRanges, CallGenotypesParam ExportMethods: callGenotypes Package: vbmp Exports: vbmp, predictCPP, predError, predLik, predClass, covParams, plotDiagnostics Package: Vega Exports: vega, plotSegmentation Package: VegaMC Exports: vegaMC, sortData Package: viper Exports: aREA, aracne2regulon, bootstrapTtest, bootstrapmsviper, distMode, fcvarna, filterCV, filterColMatrix, filterRowMatrix, frcv, frvarna, integrateSignatures, ledge, msviper, msviperAnnot, msviperCombinatorial, msviperSynergy, pruneRegulon, rowTtest, scaleGroups, shadow, signatureDistance, ttestNull, viper, viperSignature, viperSimilarity Package: vsn Exports: vsn, vsnh, vsnPlotPar, normalize.AffyBatch.vsn, vsnMatrix, justvsn, vsnrma, sagmbAssess, sagmbSimulateData, plotVsnLogLik, scalingFactorTransformation ExportMethods: vsn2, meanSdPlot, predict, logLik, coef, coefficients, show, exprs, nrow, ncol, dim, coerce ExportClasses: vsn, vsnInput Package: wateRmelon ExportMethods: naten, betaqn, nanet, nanes, danes, danet, daten1, daten2, nasen, dasen, danen, tost, fuks, swan, colnames, seabi, dmrse, dmrse_row, dmrse_col, genki, pfilter Package: wavClusteR Exports: readSortedBam, getAllSub, fitMixtureModel, getExpInterval, getHighConfSub, getClusters, filterClusters, annotateClusters, plotSizeDistribution, plotStatistics, getMetaGene, getMetaTSS, plotSubstitutions, estimateFDR, exportClusters, exportHighConfSub, exportCoverage, exportSequences Package: waveTiling Exports: cel2TilingFeatureSet, makeContrasts, makeDesign ExportMethods: getProbePosition, getNoProbes, getBetaWav, getVarBetaWav, getSmoothPar, getVarEps, getGenomeInfo, getChromosome, getStrand, getMinPos, getMaxPos, getNoLevels, getDesignMatrix, getPhenoInfo, getDataOrigSpace, getDataWaveletSpace, getWaveletFilter, getKj, getPrior, getAlpha, getDelta, getTwoSided, getSigProbes, getRegions, getGenomicRegions, getFDR, getF, getVarF, getEff, getVarEff, wfm.inference, getSigGenes, getNonAnnotatedRegions, plotWfm, getFilteredIndices, getPosition, selectProbesFromFilterOverlap, addPheno, getNoGroups, getGroupNames, getReplics, filterOverlap, selectProbesFromTilingFeatureSet, bgCorrQn, wfm.fit, show ExportClasses: WaveTilingFeatureSet, MapFilterProbe, GenomeInfo, WfmFit, WfmInf Package: webbioc Exports: installReps, mt.wrapper Package: widgetTools Exports: button, checkButton, dropdownList, entryBox, env<-, funs, funs<-, label, listBox, makeViewer, oneVScrList, pWidgets, getListOption, pWidgets<-, postFun, postFuns<-, preFun, preFuns<-, radioButton, textBox, tooltip, widget, writeList, writeText, vName, vName<-, wEnv, wEnv<-, wFuns, wFuns<-, wHeight, wHeight<-, wName, wName<-, wNotify, wNotify<-, wPostFun, wPostFun<-, wPreFun, wPreFun<-, wTitle, wTitle<-, wType, wType<-, wValue, wValue<-, wView, wView<-, safeFileOpen, widgetView, getListValue, getTextValue, getEntryValue ExportClasses: basicPW, widget, widgetView Package: xcms Exports: etg, medianFilter, retexp, specNoise, specPeaks, SSgauss, msn2xcmsRaw, verify.mzQuantML, xcmsRaw, xcmsSet, xcmsFragments, xcmsPapply ExportMethods: absent, AutoLockMass, calibrate, collect, deepCopy, filepaths, filepaths<-, diffreport, findMZ, findneutral, fillPeaks, fillPeaks.MSW, fillPeaks.chrom, findPeaks.centWave, findPeaks.massifquant, findPeaks.matchedFilter, findPeaks.MSW, findPeaks, getEIC, getPeaks, getScan, getMsnScan, getSpec, group, group.density, group.mzClust, group.nearest, groupidx, groupidx<-, groupnames, groups, groups<-, groupval, image, mzrange, peaks, peaks<-, peakTable, phenoData, phenoData<-, plotChrom, plotEIC, plotPeaks, plotRaw, plotrt, plotScan, plotSpec, plotSurf, plotTIC, plotTree, present, profinfo, profinfo<-, profMedFilt, profMethod, profMethod<-, profMz, profRange, profStep, profStep<-, progressCallback, progressCallback<-, rawEIC, rawMat, retcor, retcor.peakgroups, retcor.obiwarp, revMz, rtrange, sampclass, sampclass<-, sampnames, sampnames<-, specDist, specDist.cosine, specDist.meanMZmatch, specDist.peakCount, show, sortMz, stitch, write.cdf, write.mzdata, write.mzQuantML, xcmsSource, loadRaw ExportClasses: xcmsEIC, xcmsPeaks, xcmsRaw, xcmsSet, xcmsFragments, xcmsSource, xcmsFileSource Package: XDE Exports: calculatePosteriorAvg, empiricalStart, ssStatistic, symbolsInteresting, xde, xsScores ExportMethods: [, [[, $, bayesianEffectSize, bayesianEffectSize<-, burnin, burnin<-, calculateBayesianEffectSize, firstMcmc, firstMcmc<-, coerce, dim, directory, directory<-, featureData, featureNames, geneCenter, hyperparameters, hyperparameters<-, initialize, iterations, iterations<-, lapply, lastMcmc, lastMcmc<-, notes, nrow, nSamples, output, output<-, pData, phenotypeLabel, phenotypeLabel<-, plot, posteriorAvg, posteriorAvg<-, savedIterations, seed, seed<-, show, showIterations, showIterations<-, .standardizedDelta, standardizeSamples, studyCenter, studyNames, studyNames<-, thin, thin<-, tuning, tuning<-, updates, updates<-, zeroNu ExportClasses: ExpressionSetList, XdeParameter, XdeMcmc Package: xmapbridge Exports: xmap.debug, xmap.plot, xmap.points, xmap.col, xmap.project.new, xmap.project.load, xmap.project.list, xmap.project.save, xmap.project.delete, xmap.graph.new, xmap.graph.load, xmap.graph.list, xmap.graph.save, xmap.graph.delete, xmap.plot.new, xmap.plot.load, xmap.plot.list, xmap.plot.save, xmap.plot.delete Package: xps Exports: import.expr.scheme, import.exon.scheme, import.genome.scheme, import.data, export.scheme, export.data, export.expr, export.call, export.filter, export.root, rma, mas4, mas5, mas5.call, dabg.call, dfw, farms, ini.call, firma, firma.expr, firma.score, trma, bgcorrect, normalize, summarize, express, qualify, bgcorrect.mas4, bgcorrect.mas5, bgcorrect.rma, bgcorrect.gc, normalize.constant, normalize.quantiles, normalize.lowess, normalize.supsmu, summarize.mas4, summarize.mas5, summarize.rma, qualify.rlm, fitQC, fitRLM, rmaPLM, AffyRNAdeg, summaryAffyRNAdeg, plotAffyRNAdeg, prefilter, unifilter, plotBoxplot, plotDensity, plotImage, plotPM, plotProbeset, plotIntensity2GC, plotCorr, plotMAD, plotMA, plotNUSE, plotPCA, plotRLE, plotCall, plotBorder, plotCOI, plotVolcano, ProjectInfo, PreFilter, UniFilter, xpsQAReport, root.scheme, root.data, root.merge.data, root.expr, root.call, root.density, root.image, root.profile, root.graph1D, root.graph2D, root.mvaplot, root.hist1D, root.hist2D, root.hist3D, xpsOptions, debug.xps, getDatatype, validTreetype, getChipName, getChipType, getNameType, getProbeInfo, getNumberTrees, getTreeNames, isROOTFile, existsROOTFile, type2Exten, exonLevel, extenPart, namePart, metaProbesets ExportMethods: filterTreeset, validFilter, volcanoplot, callTreeset, exprTreeset, fcFilter, fcFilter<-, unitestFilter, unitestFilter<-, uniTest, uniTest<-, callFilter, callFilter<-, cvFilter, cvFilter<-, diffFilter, diffFilter<-, gapFilter, gapFilter<-, highFilter, highFilter<-, lowFilter, lowFilter<-, madFilter, madFilter<-, quantileFilter, quantileFilter<-, ratioFilter, ratioFilter<-, varFilter, varFilter<-, numberFilters, borderplot, borders, coiplot, NUSE, qualOption, qualOption<-, qualType, qualType<-, residuals, RLE, weights, xpsRNAdeg, attachCall, attachPVal, pvalData, pvalData<-, presCall, presCall<-, removeCall, removePVal, validCall, validPVal, callplot, attachExpr, corplot, exprs, exprs<-, exprType, exprType<-, madplot, mvaplot, normType, normType<-, nuseplot, pcaplot, rleplot, removeExpr, se.exprs, validExpr, validSE, xpsPreFilter, xpsUniFilter, addData, attachBgrd, attachDataXY, attachInten, background, background<-, bgtreeNames, indexUnits, intensity, intensity<-, intensity2GCplot, mm, mmindex, pm, pmindex, pmplot, probesetplot, rawCELName, removeBgrd, removeDataXY, removeInten, validBgrd, xpsBgCorrect, xpsDABGCall, xpsFIRMA, xpsINICall, xpsMAS4, xpsMAS5, xpsMAS5Call, xpsNormalize, xpsPreprocess, xpsQualify, xpsQualityControl, xpsSummarize, xpsRMA, attachData, boxplot, getTreeData, hist, image, mboxplot, removeData, schemeFile, schemeFile<-, schemeSet, schemeSet<-, treeData, validData, attachMask, attachProbe, attachProbeContentGC, attachProbeSequence, attachUnitNames, chipMask, chipMask<-, chipName, chipProbe, chipProbe<-, chipType, chipType<-, ncols, nrows, probeContentGC, probeInfo, probeSequence, probesetID2unitID, removeMask, removeProbe, removeProbeContentGC, removeProbeSequence, removeUnitNames, transcriptID2unitID, symbol2unitID, unitID2probesetID, unitID2symbol, unitID2transcriptID, unitNames, unitNames<-, export, fileDir, fileDir<-, initialize, root.browser, rootFile, rootFile<-, setName, setName<-, setType, setType<-, treeInfo, treeNames, arrayInfo, arrayInfo<-, authorInfo, authorInfo<-, biopsyInfo, biopsyInfo<-, cellineInfo, cellineInfo<-, datasetInfo, datasetInfo<-, hybridizInfo, hybridizInfo<-, primcellInfo, primcellInfo<-, projectInfo, projectInfo<-, sampleInfo, sampleInfo<-, show, sourceInfo, sourceInfo<-, tissueInfo, tissueInfo<-, treatmentInfo, treatmentInfo<- ExportClasses: ProjectInfo, TreeSet, Filter, PreFilter, UniFilter, SchemeTreeSet, ProcesSet, DataTreeSet, ExprTreeSet, CallTreeSet, FilterTreeSet, AnalysisTreeSet Package: XVector Exports: duplicated.XRawList, SharedVector.compare, SharedVector.copy, SharedRaw, SharedRaw.readInts, SharedRaw.writeInts, SharedRaw.read, SharedRaw.write, SharedRaw.readComplexes, XRaw, XInteger, XDouble, XNumeric, XVectorList, unlist_list_of_XVectorList, unsplit_list_of_XVectorList, RdaCollection, subseq, subseq<-, rdaPath, xvcopy, compact, reverse ExportMethods: subseq, subseq<-, rdaPath, xvcopy, compact, reverse, length, names, names<-, [, [<-, [[, [[<-, rev, as.vector, as.integer, as.numeric, as.raw, as.data.frame, toString, coerce, c, show, ==, !=, <=, duplicated, match, order, rank, is.unsorted, relist, updateObject, endoapply, showAsCell, elementLengths, width, compare, Views, viewMins, viewMaxs, viewSums, viewMeans, viewWhichMins, viewWhichMaxs, relistToClass, splitAsListReturnedClass, extractList, slice ExportClasses: SharedVector, SharedVector_Pool, SharedRaw, SharedRaw_Pool, SharedInteger, SharedDouble, XVector, XRaw, XInteger, XDouble, GroupedIRanges, XVectorList, XRawList, XIntegerViews, RdaCollection Package: yaqcaffy Exports: getSpikeProbes, getBioProbes, getRatioProbes, getQCRatios, getAllInt, probeSelectionInterface, reprodPlot, getOutliers ExportMethods: getYaqcControlProbes, info, info<-, bio, spk, deg, avns, bioCalls, gcosProbes, moreSpikeInProbes, isLog, arrays, plot, show, yaqc, merge, summary, objectVersion ExportClasses: YAQCStats, YaqcControlProbes, YaqcBioProbes, YaqcSpkProbes, YaqcDegProbes