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: 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: limma2annaffy, foldFilt, vennSelect, vennCounts2, maplot, probes2table, affystart, plotDeg, plotHist, plotPCA, hyperG2annaffy, vennSelectBM, limma2biomaRt, linksBM, annBM, foldFiltBM, probes2tableBM, vennSelectFC, hyperGoutput, getUniqueLL, writeFit, makeHmap, mirna2mrna, getMainProbes, runRomer, outputRomer, makeVenn, vennSelect2, vennPage, affyLinks, entrezLinks, goLinks

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: Agi4x44PreProcess
Exports: read.targets, read.AgilentFE, CV.rep.probes, genes.rpt.agi, BGandNorm, filter.probes, summarize.probe, build.eset, build.mappings, gsea.files, write.eset, boxplotNegCtrl, BoxPlot, ensembl.htmlpage, filter.control, filter.isfound, filter.NonUnifOL, filter.PopnOL, filter.saturated, filter.wellaboveBG, filter.wellaboveNEG, HeatMap, hierclus, MVAplotMEDctrl, MVAplotMED, PCAplot, plotDensity, RLE

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: AllelicImbalance
Exports: ASEset, ASEsetFromCountList, impBamGRL, impBamGAL, impBcfGRL, impBcfGR, decorateWithGenes, decorateWithExons, scanForHeterozygotes, getAlleleCount, getGenesFromAnnotation, getDefaultMapBiasExpMean, getDefaultMapBiasExpMean3D, getExonsFromAnnotation, getTranscriptsFromAnnotation, getCDSFromAnnotation, getGenesVector, getExonsVector, getTranscriptsVector, getCDSVector, getAnnotationDataFrame, realCigarPosition, realCigarPositions, realCigarPositionsList, getAreaFromGeneNames, getSnpIdFromLocation
ExportMethods: alleleCounts, mapBias, fraction, chisq.test, binom.test, barplot, locationplot
ExportClasses: ASEset

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, summary, metadata, supportedSeqnameMappings, findSequenceRenamingMaps, supportedSeqnameStyles, extractSeqnameSet, testSeqnames, isSupportedSeqnamesStyle, listAllSupportedStylesBySpecies, listAllSupportedSeqnameStyles, supportedSeqnames, species, cols
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, createSimpleBimap, available.db0pkgs, available.dbschemas, available.chipdbschemas, wrapBaseDBPackages, makeOrgPackageFromNCBI, makeOrgPackage, getProbeDataAffy, getProbeData_1lq, makeProbePackage
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, names, possibleDates, show, snapshotDate, snapshotDate<-, snapshotPaths, snapshotUrl, snapshotUrls, snapshotVersion

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: ASSET
Exports: h.traits, h.types, h.summary, h.forestPlot, z.max, p.dlm, p.tube

Package: attract
ExportClasses: SynExpressionSet, AttractorModuleSet

Package: BADER
Exports: BADER

Package: BAGS
Exports: DataGeneSets, Gibbs5, Gibbs4, Gibbs3, Gibbs2, MCMCDataSet, ReadGMT

Package: BaseSpaceR
Exports: ServiceURI, AppAuth, performOAuth, 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, 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, getVariantSet, getVariants, getCoverage, getCoverageStats, $, show, as.list
ExportClasses: ServiceURI, AppAuth, 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: BayesPeak
Exports: bayespeak, summarise.peaks, summarize.peaks, read.bed, plot.overfitdiag, identify.overfitdiag, region.overfitdiag, plot.bed, plot.job, plot.PP

Package: baySeq
ExportMethods: dim, [, show
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, 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, plotMAXY, normaliseIllumina, medianNormalise, calculateDetection, checkPlatform, getAnnotation, setAnnotation, beadStatusVector, illuminaOutlierMethod, squeezedVarOutlierMethod, weightsOutlierMethod, noOutlierMethod, readSampleSheet
ExportMethods: metrics, p95, snr, show, [[, dim, sectionNames, numBeads, boxplot, exprs, se.exprs, nObservations, Detection, annotation, annotation<-, se.exprs<-, exprs<-, nObservations<-, Detection<-, qcData, combine
ExportClasses: BeadLevelList, beadLevelData, ExpressionSetIllumina, illuminaChannel, beadRegistrationData

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: 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: attachAssayDataElements, BigMatrix, BigMatrixFactor, updateAssayDataElementPaths
ExportMethods: updateObject, nrow, nlevels, ncol, levels, length, dimnames, dim, as.matrix, apply, annotatedDataFrameFrom, levels<-, dimnames<-, [<-, [

Package: bioassayR
Exports: connectBioassayDB, addDataSource, loadBioassay, dropBioassay, disconnectBioassayDB, newBioassayDB, addBioassayIndex, dropBioassayIndex, activeTargets, activeAgainst, selectiveAgainst, getAssay, parsePubChemBioassay, activityMatrix
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: BioAssaySet, bioassay

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: BiocGenerics
Exports: append, as.data.frame, as.vector, cbind, rbind, 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, colnames, union, intersect, setdiff, sort, table, tapply, unique, unlist, 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
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, biocinstallRepos, useDevel, biocValid, monograph_group, RBioinf_group, biocases_group, all_group

Package: BiocParallel
Exports: MulticoreParam, SnowParam, DoparParam, SerialParam, BatchJobsParam, bplapply, bpvec, bpvectorize, bpmapply, bpaggregate, bpworkers, bpbackend, bpbackend<-, bpstart, bpstop, bpisup, bpschedule, register, registered, bpresume, bplasterror
ExportMethods: show
ExportClasses: BiocParallelParam, MulticoreParam, SnowParam, DoparParam, SerialParam, BatchJobsParam

Package: BiocStyle
Exports: latex

Package: biocViews
Exports: writeBiocViews, getBiocViews, write_VIEWS, write_REPOSITORY, genReposControlFiles, extractVignettes, extractManuals, extractNEWS, extractHTMLDocuments, extractTopLevelFiles, writeRepositoryHtml, writePackageDetailHtml, getSubTerms, getBiocSubViews, validate_bioc_views, writeTopLevelView, writeHtmlDoc, write_SYMBOLS, writeRFilesFromVignettes, getPackageNEWS, printNEWS
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
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, GENETIC_CODE, RNA_GENETIC_CODE, DNA_BASES, RNA_BASES, DNA_ALPHABET, RNA_ALPHABET, AA_ALPHABET, seqtype, seqtype<-, get_seqtype_conversion_lookup, alphabet, BString, DNAString, RNAString, AAString, BStringSet, DNAStringSet, RNAStringSet, AAStringSet, unmasked, DNAStringSetList, 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, transcribe, cDNA, dna2rna, rna2dna, codons, translate, toComplex, extractAt, replaceAt, replaceLetterAt, .inplaceReplaceLetterAt, injectHardMask, padAndClip, stackStrings, N50, width0, startIndex, endIndex, countIndex, 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, subpatterns, pattern, PhredQuality, SolexaQuality, IlluminaQuality, 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, countIndex, 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, seqtype, seqtype<-, updateObject, append, splitAsListReturnedClass, union, intersect, setdiff, setequal, %in%, match, compare, 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: 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, 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: BRAIN
Exports: getAtomsFromSeq, useBRAIN, calculateIsotopicProbabilities, calculateAverageMass, calculateMonoisotopicMass, calculateNrPeaks

Package: BrainStars
Exports: getBrainStars, getBrainStarsFigure

Package: bridge
Exports: bridge.2samples, bridge.3samples

Package: BSgenome
Exports: installed.genomes, available.genomes, GenomeDescription, newSNPlocs, BSgenome, installed.SNPs, available.SNPs, bsapply, GenomeData, GenomeDataList, organism, species, provider, providerVersion, releaseDate, releaseName, bsgenomeName, referenceGenome, compatibleGenomes, snpcount, snplocs, snpid2loc, snpid2alleles, snpid2grange, sourceUrl, SNPlocs, SNPlocs_pkgname, SNPcount, mseqnames, masknames, injectSNPs, gdapply, gdApply, gdReduce, gdreduce, forgeSeqlengthsFile, forgeSeqFiles, forgeMasksFiles, forgeBSgenomeDataPkg
ExportMethods: names, show, length, [[, $, score, getSeq, matchPWM, countPWM, vmatchPattern, vcountPattern, organism, species, provider, providerVersion, releaseDate, releaseName, bsgenomeName, seqinfo, seqinfo<-, seqnames, referenceGenome, compatibleGenomes, snpcount, snplocs, snpid2loc, snpid2alleles, snpid2grange, sourceUrl, SNPlocs, SNPlocs_pkgname, SNPcount, mseqnames, masknames, injectSNPs, gdapply, gdReduce, forgeBSgenomeDataPkg
ExportClasses: GenomeDescription, SNPlocs, InjectSNPsHandler, BSgenome, 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
ExportMethods: bumphunter

Package: BUS
Exports: BUS, pred.network, gene.similarity, gene.trait.similarity, gene.pvalue, gene.trait.pvalue

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: calcDenovo, calcExp, createDenovoGenome, denovoExpr, getDistrs, getIsland, genePlot, getRoc, mergeBatches, mergeExp, modelPrior, pathCounts, plotPriorAS, posprob, probNonEquiv, procBam, procGenome, relativeExpr, rmShortInserts, simMultSamples, simReads, transcripts, variants, variants<-, getReads, getNreads, getChr, getIsland, subsetGenome, txLength, wrapKnown
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: 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

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

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, 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, 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, bufferLines, bufferResultSet, parBatchByIndex, batchByIndex, selectInBatches, dbTransaction
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, ap
ExportClasses: SDFstr, SDF, SDFset, SMI, SMIset, AP, APset, FP, FPset

Package: chimera
Exports: plotCoverage, is.fSet

Package: chipenrich
Exports: chipenrich, plot_spline_length, plot_dist_to_tss, 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: 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, addProteinNames, networkView, easyEditor, getMappingFile, formatPINAPPI, formatSTRINGPPI, formatiRefIndex, combinePPI

Package: cleanUpdTSeq
Exports: BED2GRangesSeq, getUpstreamSequence, getDownstreamSequence, buildFeatureVector, predictTestSet

Package: cleaver
ExportMethods: cleave

Package: clippda
Exports: sampleClusteredData, negativeIntensitiesCorrection
ExportMethods: show
ExportClasses: aclinicalProteomicsData

Package: clipper
Exports: cliqueVarianceTest, cliqueMeanTest, getGraphEntryGenes, getJunctionTreePaths, pathQ, clipper, prunePaths, easyClip, plotInCytoscape, nameCliques, deleteEdge, easyLook

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: buildGOmap, compareCluster, enrichGO, enrichKEGG, Gff2GeneTable, groupGO, plot
ExportMethods: summary
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: 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
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: 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

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, GAPS, calcCoGAPSStat, plotGAPS, ReadCoGAPSResults, plotSmoothPatterns, reorderByPatternMatch

Package: coGPS
Exports: PCOPA, PatientSpecificGeneList, PlotTopPCOPA, plotCOPA, permCOPA

Package: ConsensusClusterPlus
Exports: ConsensusClusterPlus, calcICL

Package: copa
Exports: copa, plotCopa, copaPerm, tableCopa, scatterPlotCopa, summaryCopa

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: Cormotif
Exports: cormotiffit, cormotiffitall, cormotiffitfull, cormotiffitsep, generank, plotIC, plotMotif

Package: CorMut
Exports: seqFormat, kaksCodon, kaksAA, ckaksCodon, ckaksAA, miCodon, miAA, biCkaksCodon, biCkaksAA, biMICodon, biMIAA, seq_num, kaks, lod, q, ka, ks, mi, p.value, ckaks, method, positiveSite01, positiveSite02, state_1, statistic_1, state_2, statistic_2
ExportMethods: filterSites, plot, biCompare
ExportClasses: kaksCodon, kaksAA, ckaks, MI, biCkaksCodon, biCkaksAA, biMICodon, biMIAA

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: 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: 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: 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, annotation, genes, isoforms, TSS, CDS, promoters, splicing, relCDS, fpkm, repFpkm, count, distValues, csDensity, csScatter, csVolcano, csBoxplot, csHeatmap, 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
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, DB2FASTA, FormGroups, IdentifyByRank, IdLengths, TerminalChar, DistanceMatrix, IdClusters, MODELS, ConsensusSequence, IdConsensus, TileSeqs, FindChimeras, CreateChimeras, DesignArray, Array2Matrix, NNLS, CalculateEfficiencyArray, CalculateEfficiencyPCR, DesignPrimers, CalculateEfficiencyFISH, DesignProbes, BrowseSequences, BrowseDB, AlignSeqs, AlignProfiles, MaskAlignment

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: 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: 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: DESeq, DESeqDataSet, DESeqDataSetFromHTSeqCount, DESeqDataSetFromMatrix, estimateDispersionsFit, estimateDispersionsGeneEst, estimateDispersionsMAP, estimateSizeFactorsForMatrix, getVarianceStabilizedData, makeExampleDESeqDataSet, nbinomLRT, nbinomWaldTest, plotDispEsts, plotMA, plotPCA, removeResults, replaceOutliersWithTrimmedMean, results, resultsNames, rlogData, rlogTransformation, varianceStabilizingTransformation
ExportMethods: sizeFactors, plotMA, plotDispEsts, normalizationFactors, estimateSizeFactors, estimateDispersions, dispersions, dispersionFunction, design, counts, sizeFactors<-, normalizationFactors<-, dispersions<-, dispersionFunction<-, design<-, counts<-
ExportClasses: DESeqDataSet

Package: DEXSeq
Exports: newExonCountSet, geneIDs, geneIDs<-, exonIDs, exonIDs<-, subsetByGenes, geneCountTable, countTableForGene, modelFrameForGene, estimateExonDispersionsForModelFrame_BM, fitDispersionFunction, read.HTSeqCounts, DEXSeqHTML, DEUresultTable, plotDEXSeq, estimatelog2FoldChanges, doCompleteDEUAnalysis, makeCompleteDEUAnalysis_BM, constructModelFrame, estimateDispersions, testForDEU, estimateDispersions_BM, testGeneForDEU_BM, testForDEU_BM, perGeneQValue, countReadsForDEXSeq, buildExonCountSet, prepareAnnotationForDEXSeq
ExportMethods: counts, counts<-, [, sizeFactors, sizeFactors<-, design, design<-, estimateSizeFactors, estimateDispersions, plotDispEsts, plotMA
ExportClasses: ExonCountSet

Package: dexus
Exports: conditionSizes, 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_SN_RATIO, DBA_OLAP_PEAKS, DBA_OLAP_ALL, DBA_OLAP_RATE, 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_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_DATA_FRAME, DBA_DATA_RANGEDDATA, DBA_DATA_GRANGES, DBA_DATA_SUMMARIZED_EXPERIMENT
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: 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: DOSE
Exports: ALLEXTID, EXTID2NAME, EXTID2TERMID, TERM2NAME, TERMID2EXTID, doSim, enrich.internal, enrichDO, 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, 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: 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: chastityFilter, naPositionFilter
ExportMethods: transcriptCounts, strand, reduce, readLength, readCoverage, readCounts, ranges, plotNormalizationFactors, plotDispersionEstimates, plotDispLSD, parallelize, organismName, multivariateConditions, librarySize, knownOrganisms, genomicAnnotation, geneModel, geneCounts, fileName, fetchCoverage, fetchAnnotation, featureCounts, exonCounts, easyRNASeq, demultiplex, count, colnames, chrSize, barcodePlot, RPKM, strand<-, readLength<-, readCoverage<-, readCounts<-, organismName<-, librarySize<-, genomicAnnotation<-, geneModel<-, fileName<-, chrSize<-
ExportClasses: RNAseq

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, print.Image, as.raster.Image, Grayscale, Color, colorMode, colorMode<-, imageData, imageData<-, getFrame, getNumberOfFrames, readImage, writeImage, display, resize, rotate, flip, flop, translate, affine, transpose, thresh, bwlabel, watershed, propagate, ocontour, paintObjects, rmObjects, reenumerate, colorLabels, median.Image, quantile.Image, filter2, gblur, medianFilter, makeBrush, erode, dilate, opening, closing, erodeGreyScale, dilateGreyScale, openingGreyScale, closingGreyScale, whiteTopHatGreyScale, blackTopHatGreyScale, selfcomplementaryTopHatGreyScale, distmap, floodFill, fillHull, rgbImage, channel, stackObjects, tile, untile, drawfont, drawtext, drawCircle, computeFeatures, computeFeatures.basic, computeFeatures.shape, computeFeatures.moment, computeFeatures.haralick, standardExpandRef, localCurvature, blur, equalize, drawtext, drawfont, getFeatures, hullFeatures, zernikeMoments, edgeProfile, edgeFeatures, haralickFeatures, haralickMatrix, moments, cmoments, smoments, rmoments
ExportMethods: 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

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
ExportClasses: SeqExpressionSet

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: ENVISIONQuery
Exports: getServices, getServiceNames, getService, getServiceOptions, getToolNames, getTool, getServiceClient, getInputTypes, ENVISIONQuery

Package: epigenomix
Exports: chipVals, chipVals<-, chains, classification, components, convergence, mmData, listClassificationMethods, weights, bayesMixModel, integrateData, matchProbeToPromoter, mlMixModel, normalizeChIP, plotChains, plotClassification, plotComponents, summarizeReads
ExportMethods: dim, length, show, summary
ExportClasses: ChIPseqSet, MixModel, MixModelBayes, MixModelML, MixtureComponent

Package: epivizr
Exports: startEpiviz
ExportClasses: EpivizDeviceMgr, EpivizData, EpivizTrackData, EpivizFeatureData, EpivizBlockData, EpivizBpData

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: 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: query_gtLinker, getResults_gtLinker, query_david, getResults_david, adjMatrix, toMatrix, functionalNetwork, intersectionNetwork, plotMetagroupsDistance, report_gtLinker, report_david, getTerms

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: 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, curv1Filter, curv2Filter, 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
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, curv1Filter, curv2Filter, 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: 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: 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: ReadDD, KmeansMeanSD, KmeansMedianrSD, MFI2MESF, lrMESF, qrMESF, DiscriminantExamination, gPS, MultilevelgPS, MultilevelrPS, qrWEIGHTEDMESF, rPS

Package: flowStats
Exports: lymphGate, lymphFilter, oneDGate, quadrantGate, rangeGate, rangeFilter, warpSet, proBin, binByRef, gaussNorm, plotBins, calcPearsonChi, calcPBChiSquare, gpaSet, iProcrustes, normQA, singletGate
ExportMethods: %in%, normalize
ExportClasses: lymphFilter, rangeFilter

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, testGatingCompliance

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: ncFlowSet<-, archive, booleanFilter, char2booleanFilter, flowWorkspace.par.get, flowWorkspace.par.set, GatingSetList, getChannelMarker, getFJWSubsetIndices, getIndiceMat, isNcdf, load_gs, load_gslist, mkformula, save_gs, save_gslist, unarchive
ExportMethods: summary, show, setNode, setGate, sampleNames, recompute, plotPopCV, plotGate, plot, pData, parseWorkspace, openWorkspace, ncFlowSet, length, lapply, keyword, getTransformations, getTotal, getSamples, getSampleGroups, getSample, getProp, getPopStats, getParent, getNodes, getKeywords, getIndices, getGate, getData, getCompensationMatrices, getChildren, GatingSet, flowData, closeWorkspace, clone, add, pData<-, ncFlowSet<-, flowData<-, [[, [
ExportClasses: GatingSetList, GatingSet, GatingHierarchy, flowJoWorkspace, booleanFilter

Package: fmcsR
Exports: fmcs, fmcsBatch, plotMCS, mcs2sdfset
ExportMethods: stats, mcs1, mcs2, [[, coerce, show
ExportClasses: MCS

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, 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: gCMAP
Exports: annotate_eset_list, center_eSet, eSetOnDisk, generate_gCMAP_NChannelSet, eset_instances, 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: 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, 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: 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: 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: 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: GenomicFeatures
Exports: loadFeatures, transcripts_deprecated, exons_deprecated, introns_deprecated, 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, transcriptWidths, transcriptLocs2refLocs, extractTranscripts, extractTranscriptsFromGenome, sortExonsByRank, makeFeatureDbFromUCSC, makeTxDbPackage, makeTxDbPackageFromUCSC, makeTxDbPackageFromBiomart, makeFDbPackageFromUCSC, features, supportedMiRBaseBuildValues, getPromoterSeq
ExportMethods: saveFeatures, metadata, show, as.list, seqinfo, seqinfo<-, transcripts, exons, cds, genes, promoters, disjointExons, microRNAs, tRNAs, transcriptsByOverlaps, exonsByOverlaps, cdsByOverlaps, transcriptsBy, exonsBy, cdsBy, intronsByTranscript, fiveUTRsByTranscript, threeUTRsByTranscript, isActiveSeq, isActiveSeq<-, asBED, asGFF, determineDefaultSeqnameStyle, findSpliceOverlaps, getPromoterSeq, distance
ExportClasses: TranscriptDb, FeatureDb

Package: GenomicRanges
Exports: duplicated.GenomicRanges, phicoef, validCigar, CIGAR_OPS, explodeCigarOps, explodeCigarOpLengths, cigarToRleList, splitCigar, cigarRangesAlongReferenceSpace, cigarRangesAlongQuerySpace, cigarRangesAlongPairwiseSpace, extractAlignmentRangesOnReference, cigarToIRanges, cigarToIRangesListByAlignment, cigarToIRangesListByRName, cigarWidthAlongReferenceSpace, cigarWidthAlongQuerySpace, cigarWidthAlongPairwiseSpace, cigarToWidth, cigarToQWidth, cigarNarrow, cigarQNarrow, cigarOpTable, cigarToCigarTable, summarizeCigarTable, queryLoc2refLoc, queryLocs2refLocs, makeSeqnameIds, Seqinfo, GRanges, GRangesList, GenomicRangesList, GIntervalTree, .DollarNames.GenomicRanges, makeGRangesFromDataFrame, makeGRangesListFromFeatureFragments, tileGenome, makeGAlignmentsListFromFeatureFragments, GAlignments, readGAlignments, GAlignmentPairs, readGAlignmentPairs, GappedAlignments, readGappedAlignments, GappedAlignmentPairs, readGappedAlignmentPairs, GAlignmentsList, readGAlignmentsList, flipQuery, selectEncodingWithCompatibleStrand, extractQueryStartInTranscript, countCompatibleOverlaps, Union, IntersectionNotEmpty, IntersectionStrict, keepSeqlevels, dropSeqlevels, renameSeqlevels, restoreSeqlevels, checkConstraint, seqinfo, seqinfo<-, seqnames, seqnames<-, seqlevels, seqlevels<-, sortSeqlevels, seqlevelsInUse, seqlevels0, seqlengths, seqlengths<-, isCircular, isCircular<-, genome, genome<-, seqnameStyle, seqnameStyle<-, rname, rname<-, cigar, qwidth, qnarrow, grglist, granges, introns, rglist, first, last, left, right, isProperPair, SummarizedExperiment, exptData, exptData<-, rowData, rowData<-, colData, colData<-, assays, assays<-, assay, assay<-, summarizeOverlaps, isCompatibleWithSplicing, isCompatibleWithSkippedExons, extractSteppedExonRanks, extractSpannedExonRanks, extractSkippedExonRanks, findCompatibleOverlaps, findSpliceOverlaps
ExportMethods: checkConstraint, seqinfo, seqinfo<-, seqnames, seqnames<-, seqlevels, seqlevels<-, sortSeqlevels, seqlevelsInUse, seqlengths, seqlengths<-, isCircular, isCircular<-, genome, genome<-, seqnameStyle, seqnameStyle<-, rname, rname<-, cigar, qwidth, qnarrow, grglist, granges, introns, rglist, first, last, left, right, isProperPair, SummarizedExperiment, exptData, exptData<-, rowData, rowData<-, colData, colData<-, assays, assays<-, assay, assay<-, summarizeOverlaps, isCompatibleWithSplicing, isCompatibleWithSkippedExons, extractSteppedExonRanks, extractSpannedExonRanks, extractSkippedExonRanks, findCompatibleOverlaps, findSpliceOverlaps, length, names, names<-, dimnames<-, [, [<-, [[, [[<-, $, $<-, as.data.frame, coerce, c, cbind, rbind, show, ==, <=, duplicated, match, %in%, order, sort, rank, union, intersect, setdiff, start, end, split, unlist, range, Ops, merge, updateObject, strand, strand<-, elementMetadata, elementMetadata<-, mcols, mcols<-, values, values<-, splitAsListReturnedClass, width, start<-, width<-, end<-, compare, ranges, ranges<-, map, ngap, score, shift, narrow, flank, resize, promoters, restrict, reduce, gaps, disjoin, isDisjoint, disjointBins, punion, pintersect, psetdiff, pgap, findOverlaps, countOverlaps, overlapsAny, subsetByOverlaps, precede, follow, nearest, distance, distanceToNearest, encodeOverlaps, coverage
ExportClasses: Constraint, ConstraintORNULL, Seqinfo, GenomicRanges, GenomicRangesORmissing, GRanges, GRangesList, GIntervalTree, GenomicRangesORGRangesList, GAlignments, GAlignmentPairs, GAlignmentsList, GappedAlignments, GappedAlignmentPairs, SummarizedExperiment, Assays, GenomicRangesList, SimpleGenomicRangesList

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: baf<-, chrNames<-, cn<-, locData<-, lrr<-, baf, baf2mbaf, BAFSet.to.ExpressionSets, BAFSet, boundingIndices, boundingIndices2, boundingIndicesByChr, bounds2Rle, calcGC, chr, chrIndices, chrInfo, chrNames, chrOrder, cn, cn2lr, CNSet, colMeans, fixSegNAs, gcCorrect, genomeAxis, genoPlot, genoPos, GenoSet, isGenomeOrder, locData, lr2cn, lrr, modeCenter, pos, rangeColMeans, rangeSampleMeans, readGenoSet, runCBS, segPairTable, segs2Granges, segs2RangedData, segs2Rle, segs2RleDataFrame, segTable, subsetAssayData, toGenomeOrder
ExportMethods: universe, show, sampleNames, rownames, rangeSegMeanLength, nrow, names, genome, featureNames, elementLengths, dim, colnames, [
ExportClasses: GenoSet, CNSet, BAFSet

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
ExportClasses: smlSet, probeId, rsid

Package: ggbio
Exports: arrangeGrobByParsingLegend, ggbio, GGbio, scale_x_sequnit, scale_fill_giemsa, scale_fill_fold_change, 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, nolegend, ggsave
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, mold, fixed, fixed<-, xlim, xlim<-, reset, backup, bgColor, bgColor<-, labeled, labeled<-, mutable, mutable<-, height, height<-, hasAxis, hasAxis<-, ggplot

Package: GGtools
Exports: 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, bindmaf, 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
ExportMethods: 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: eqtlTestsManager, eqtlEstimatesManager, mcwBestCis, gwSnpScreenResult, transManager, allSigCis, sensiCisInput, sensiCisOutput, mcwAllCis, cisRun, CisConfig

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: 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: 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, 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: 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: 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, AnnotationTrack, DetailsAnnotationTrack, BiomartGeneRegionTrack, DataTrack, DisplayPars, drawGD, GeneRegionTrack, GenomeAxisTrack, IdeogramTrack, UcscTrack, as.list, availableDefaultMapping, availableDisplayPars, clearSessionCache, exportTracks, plotTracks, SequenceTrack
ExportMethods: [, as.list, chromosome, chromosome<-, coerce, consolidateTrack, coords, coverage, displayPars, displayPars<-, elementMetadata<-, 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, AnnotationTrack, DetailsAnnotationTrack, BiomartGeneRegionTrack, DataTrack, DisplayPars, GeneRegionTrack, GenomeAxisTrack, IdeogramTrack, ImageMap, SequenceTrack

Package: gwascat
Exports: locs4trait, topTraits, elementMetadata, ranges, chklocs, riskyAlleleCount, getRsids, getTraits, subsetByChromosome, subsetByTraits, obo2graphNEL, makeCurrentGwascat, traitsManh, gwcex2gviz
ExportMethods: getRsids, [, getTraits, subsetByChromosome, subsetByTraits
ExportClasses: gwaswloc

Package: GWASTools
Exports: SnpAnnotationDataFrame, SnpAnnotationSQLite, ScanAnnotationDataFrame, ScanAnnotationSQLite, NcdfReader, NcdfGenotypeReader, GdsReader, GdsGenotypeReader, MatrixGenotypeReader, NcdfIntensityReader, GenotypeData, IntensityData, alleleFrequency, anomSegmentBAF, anomFilterBAF, anomDetectBAF, anomDetectLOH, anomIdentifyLowQuality, anomSegStats, anomStatsPlot, apartSnpSelection, asSnpMatrix, assocTestCPH, assocTestFisherExact, assocTestRegression, BAFfromClusterMeans, BAFfromGenotypes, batchChisqTest, batchFisherTest, checkNcdfGds, chromIntensityPlot, convertGdsNcdf, convertNcdfGds, convertVcfGds, duplicateDiscordance, duplicateDiscordanceAcrossDatasets, duplicateDiscordanceProbability, findBAFvariance, gdsSetMissingGenotypes, genoClusterPlot, genoClusterPlotByBatch, genotypeToCharacter, gwasExactHW, hetByScanChrom, hetBySnpSex, ibdAreasDraw, ibdAssignRelatedness, ibdPlot, intensityOutliersPlot, manhattanPlot, meanIntensityByScanChrom, meanSdByChromWindow, medianSdOverAutosomes, mendelErr, mendelList, mendelListAsDataFrame, minorAlleleDetectionAccuracy, missingGenotypeByScanChrom, missingGenotypeBySnpSex, ncdfAddData, ncdfAddIntensity, ncdfCheckGenotype, ncdfCheckIntensity, ncdfCreate, ncdfImputedDosage, ncdfSetMissingGenotypes, ncdfSubset, ncdfSubsetCheck, pedigreeCheck, pedigreeClean, pedigreeDeleteDuplicates, pedigreeFindDuplicates, pedigreeMaxUnrelated, pedigreePairwiseRelatedness, plinkCheck, plinkToNcdf, plinkWrite, pseudoautoIntensityPlot, qqPlot, qualityScoreByScan, qualityScoreBySnp, sdByScanChromWindow, simulateGenotypeMatrix, simulateIntensityMatrix, snpCorrelationPlot, allequal, getobj, saveas, readWriteFirst
ExportMethods: getAlleleA, getAlleleB, getAnnotation, getAttribute, getBAlleleFreq, getChromosome, getDimension, getDimensionNames, getGenotype, getLogRRatio, getMetadata, 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, GdsReader, GdsGenotypeReader, MatrixGenotypeReader, NcdfIntensityReader, 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: 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: HilbertVis
Exports: hilbertCurve, hilbertCurvePoint, plotHilbertCurve, shrinkVector, plotLongVector, makeWiggleVector, hilbertImage, makeRandomTestData, showHilbertImage

Package: HilbertVisGUI
Exports: simpleLinPlot, hilbertDisplay, hilbertDisplayThreeChannel, dotsapply

Package: HiTC
Exports: binningC, CQC, intervalsDist, discretize, exportC, export.my5C, importC, import.my5C, extractRegion, getExpectedCounts, HTCexp, HTClist, pca.hic, removeIntervals, setIntervalScale
ExportMethods: as.list, c, detail, show, intdata, intdata<-, isBinned, isIntraChrom, isSymmetric, y_intervals, y_intervals<-, x_intervals, x_intervals<-, xy_intervals, id, 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: alignReads, analyzeVariants, bamCountUniqueReads, buildConfig, buildGenomicFeaturesFromTxDb, calculateCoverage, calculateTargetLengths, checkConfig, checkGATKJar, checkPicardJar, computeBamStats, computeCoverage, consolidateByRead, countGenomicFeatures, countGenomicFeaturesChunk, detectAdapterContam, detectQualityInFASTQFile, detectRRNA, FastQStreamer.getReads, FastQStreamer.init, FastQStreamer.release, filterByLength, filterQuality, gatk, getBams, getChunkDirs, getConfig.integer, getConfig.logical, getConfig.numeric, getConfig.vector, getConfig, getEndNumber, getMemoryUsage, getNumberOfReadsInFASTQFile, getNumericVectorDataFromFile, getObjectFilename, getPackageFile, getRDataFromFile, 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, plotDepthByStrand, plotDF, preprocessReads, processChunks, readInputFiles, readRNASeqEnds, relativeBarPlot, removeChunkDir, resource, rpkm, runAlignment, runPipeline, runPipelineConfig, runPreprocessReads, safeExecute, safeUnlink, saveWithID, sclapply, setUpDirs, setupTestFramework, statCountFeatures, TP53GenomicFeatures, traceMem, trimReads, trimTailsByQuality, truncateReads, tryKeepTraceback, updateConfig, vcfStat, wrap.callVariants, writeAudit, writeConfig, writeFastQFiles, 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<-
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: 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: impute
Exports: impute.knn

Package: inSilicoDb
Exports: getPlatforms, getDataset, getDatasets, getAnnotations, getDatasetList

Package: inSilicoMerging
Exports: merge, plotMDS, plotRLE, plotGeneWiseBoxPlot

Package: intansv
Exports: methodsMerge, plotChromosome, plotRegion, readBreakDancer, readCnvnator, readDelly, readPindel, readSvseq, svAnnotation, geneAnnotation, readLumpy, readSoftSearch

Package: interactiveDisplay
ExportMethods: gridsvgjs, 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: aggregate.Rle, as.data.frame.DataFrame, as.data.frame.DataFrameList, as.data.frame.GappedRanges, as.data.frame.Hits, as.data.frame.OverlapEncodings, as.data.frame.RangedData, as.data.frame.Ranges, as.data.frame.RangesList, as.data.frame.Rle, as.data.frame.Vector, as.list.List, as.list.SimpleList, as.list.CompressedList, as.list.Rle, as.list.CompressedNormalIRangesList, as.list.Hits, diff.Rle, duplicated.Vector, duplicated.Ranges, duplicated.Dups, duplicated.DataTable, duplicated.Rle, duplicated.AtomicList, duplicated.CompressedAtomicList, head.Vector, levels.Rle, levels.OverlapEncodings, mean.Rle, median.Rle, quantile.Rle, rev.Rle, sort.Vector, sort.Rle, sort.RleList, summary.Rle, tail.Vector, unique.Vector, unique.DataTable, unique.Rle, unique.CompressedAtomicList, unique.CompressedRleList, unique.SimpleRleList, window.Vector, window.vector, window.factor, window.NULL, window.Rle, window<-.Vector, window<-.vector, window<-.factor, setValidity2, new2, setMethods, .Call2, isTRUEorFALSE, isSingleInteger, isSingleNumber, isSingleString, isSingleNumberOrNA, isSingleStringOrNA, recycleIntegerArg, recycleNumericArg, fold, safeExplode, strsplitAsListOfIntegerVectors, svn.time, subsetByRanges, multisplit, seqapply, mseqapply, tseqapply, seqsplit, seqby, splitAsList, solveUserSEW0, IRanges, solveUserSEW, successiveIRanges, breakInChunks, whichAsIRanges, asNormalIRanges, rangeComparisonCodeToLetter, IntervalTree, IntervalForest, H2LGrouping, Dups, PartitioningByEnd, PartitioningByWidth, RangedData, RangedDataList, RangedSelection, FilterRules, FilterMatrix, RDApplyParams, RangesList, IRangesList, RleViewsList, remapHits, CompressedHitsList, hits, %over%, %within%, %outside%, encodeOverlaps1, RangesList_encodeOverlaps, MaskCollection.show_frame, Mask, read.gapMask, read.agpMask, read.liftMask, read.rmMask, read.trfMask, newViews, successiveViews, SimpleList, DataFrame, LogicalList, IntegerList, NumericList, ComplexList, CharacterList, RawList, RleList, DataFrameList, SplitDataFrameList, get_showHeadLines, get_showTailLines, isConstant, endoapply, mendoapply, runsum, runmean, runwtsum, runq, metadata, metadata<-, showAsCell, elementMetadata, elementMetadata<-, mcols, mcols<-, values, values<-, rename, seqselect, seqselect<-, splitAsListReturnedClass, mstack, shiftApply, elementType, elementLengths, isEmpty, revElements, as.env, width, mid, start<-, width<-, end<-, isNormal, whichFirstNotNormal, compare, selfmatch, findMatches, countMatches, 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, runLength, runValue, nrun, runLength<-, runValue<-, Rle, findRange, findRun, splitRanges, 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<-, queryHits, subjectHits, queryLength, subjectLength, countQueryHits, countSubjectHits, map, pmap, Loffset, Roffset, encoding, flippedQuery, Lencoding, Rencoding, Lngap, Rngap, shift, narrow, flank, reflect, resize, promoters, restrict, threebands, reduce, gaps, disjoin, isDisjoint, disjointBins, punion, pintersect, psetdiff, pgap, findOverlaps, countOverlaps, overlapsAny, subsetByOverlaps, precede, follow, nearest, distance, distanceToNearest, encodeOverlaps, reverse, coverage, slice, expand, classNameForDisplay
ExportMethods: isConstant, endoapply, mendoapply, runsum, runmean, runwtsum, runq, metadata, metadata<-, showAsCell, elementMetadata, elementMetadata<-, mcols, mcols<-, values, values<-, rename, seqselect, seqselect<-, splitAsListReturnedClass, mstack, shiftApply, elementType, elementLengths, isEmpty, revElements, as.env, width, mid, start<-, width<-, end<-, isNormal, whichFirstNotNormal, compare, selfmatch, findMatches, countMatches, 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, runLength, runValue, nrun, runLength<-, runValue<-, Rle, findRange, findRun, splitRanges, 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<-, queryHits, subjectHits, queryLength, subjectLength, countQueryHits, countSubjectHits, map, pmap, Loffset, Roffset, encoding, flippedQuery, Lencoding, Rencoding, Lngap, Rngap, shift, narrow, flank, reflect, resize, promoters, restrict, threebands, reduce, gaps, disjoin, isDisjoint, disjointBins, punion, pintersect, psetdiff, pgap, findOverlaps, countOverlaps, overlapsAny, subsetByOverlaps, precede, follow, nearest, distance, distanceToNearest, encodeOverlaps, reverse, coverage, slice, expand, classNameForDisplay, length, length<-, names, names<-, nrow, NROW, ncol, NCOL, dim, rownames, rownames<-, colnames, colnames<-, dimnames, dimnames<-, [, [<-, [[, [[<-, $, $<-, as.vector, as.logical, as.integer, as.numeric, as.complex, as.character, as.raw, as.factor, as.matrix, as.data.frame, as.list, as.table, coerce, c, show, ==, !=, <=, >=, <, >, duplicated, match, %in%, order, sort, rank, is.unsorted, Ops, Math, Math2, Summary, Complex, summary, rev, rep, head, tail, drop, start, end, min, max, range, which.max, which.min, diff, mean, var, cov, cor, sd, median, quantile, mad, IQR, smoothEnds, runmed, subset, window, window<-, aggregate, nchar, substr, substring, chartr, tolower, toupper, sub, gsub, levels, levels<-, unlist, stack, split<-, unsplit, relist, update, append, !, which, ifelse, merge, split, with, within, t, is.na, na.omit, na.exclude, complete.cases, by, cbind, rbind, eval, lapply, sapply, mapply, pmax, pmin, pmax.int, pmin.int, paste, Reduce, Filter, Find, Map, Position, rep.int, table, tapply, union, intersect, setdiff, unique, xtabs, updateObject
ExportClasses: characterORNULL, functionORNULL, Annotated, DataTable, DataTableORNULL, Vector, List, SimpleList, CompressedList, Ranges, RangesORmissing, IRanges, NormalIRanges, IntervalTree, IntervalForest, Grouping, H2LGrouping, Dups, Partitioning, PartitioningByEnd, PartitioningByWidth, Views, Rle, 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, DataFrame, DataFrameList, SimpleDataFrameList, SplitDataFrameList, CompressedSplitDataFrameList, SimpleSplitDataFrameList, RangedData, RangedDataList, FilterRules, FilterMatrix, RDApplyParams, Hits, HitsList, CompressedHitsList, OverlapEncodings, RangedSelection, RangesMapping

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: 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, download_KEGGfile, find_enriched_pathway, parse_XMLfile, plot_pathway, 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: 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: 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: 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: 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: metaArray
Exports: poe.mcmc, poe.em, intcor

Package: metagenomeSeq
Exports: aggregateM, cumNorm, cumNormMat, cumNormStat, exportMat, exportStats, fitZig, load_meta, load_metaQ, load_phenoData, MRcoefs, MRfisher, MRfulltable, MRtable, plotCorr, plotGenus, plotMRheatmap, plotOTU, plotOrd, plotRare, zigControl, newMRexperiment, MRcounts, posterior.probs, normFactors, libSize, expSummary
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: metaSeq
Exports: meta.readData, meta.oneside.noiseq, Fisher.test, Stouffer.test, other.oneside.pvalues

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
ExportMethods: asBigMatrix, exprs, exprs<-, methylated, unmethylated, detection, methylated<-, unmethylated<-, detection<-, getHistory, combine, [, coerce, locData, locData<-, chrNames
ExportClasses: MethyGenoSet

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, mfuzz, mfuzz.plot, mfuzz.plot2, Mfuzzgui, mfuzzColorBar, overlap, overlap.plot, partcoef, randomise, standardise, standardise2, top.count, table2eset

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: 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, dropMethylationLoci, getLocations, getAnnotation, mapToGenome, getIslandStatus, getProbeType, getSnpInfo, addSnpInfo, normalize.illumina.control, bgcorrect.illumina, preprocessRaw, preprocessIllumina, preprocessSWAN, preprocessQuantile, 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: callDenovoSegments, concAtTop, TrioSet, TrioSetList, TrioSetListLD, correspondingCall, discAtTop, isDenovo, narrow, narrowRanges, Pedigree, stackRangedDataList, xyplotTrio, xypanelTrio, xyplotTrioLrrBaf
ExportMethods: [, allNames, annotatedDataFrameFrom, calculateMindist, coerce, computeBayesFactor, dims, fatherNames, fatherPhenoData, motherPhenoData, phenoData, mindist, mindist<-, mad2, MAP, motherNames, ncol, nrow, offspringNames, offspringPhenoData, order, pedigree, segment2, trios, updateObject, width, initialize, gcSubtract

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: 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, plot, plotXvalRDA, makeLearnerSchema, standardMLIConverter, sldaI, fs.absT, fs.probT, ksvmI, knn.cvI, knn.cv2, adaI, fs.topVariance, hclustI, kmeansI, pamI, blackboostI, gbm2, BgbmI, plsdaI
ExportMethods: show, RObject, confuMat, trainInd, precision, recall, macroF1, 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: MMDiff
Exports: getPeakProfiles, findOutliers, getNormFactors, compHistDists, detPeakPvals, plotHistDists, plotPeak

Package: MmPalateMiRNA
Exports: imputeKNN, fixOutliers, fixMVs, clustPlot
ExportMethods: densityplot, levelplot, checkOutliers, checkMVs, filterArray, MADvsMedianPlot, MAplot

Package: mosaics
Exports: constructBins, readBins, mosaicsFit, mosaicsPeak, mosaicsRunAll, generateWig, 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, 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: msmsEDA
Exports: pp.msms.data, gene.table, count.stats, counts.pca, counts.hc, norm.counts, counts.heatmap, disp.estimates

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
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, clean, removePeaks, removeReporters, 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
ExportClasses: pSet, MIAPE, MSnExp, MSnProcess, MSnSet, Spectrum, Spectrum1, Spectrum2, ReporterIons

Package: Mulcom
Exports: mulCalc, mulDiff, mulFSG, mulOptPars, mulOptPlot, mulOpt, mulPerm, mulScores, mulCAND, mulDELTA, mulParOpt, mulInt, mulIndex
ExportClasses: MULCOM, MULCOM_P

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: mzID
Exports: mzID
ExportMethods: flatten
ExportClasses: mzID

Package: mzR
Exports: openMSfile
ExportMethods: close, isInitialized, initializeRamp, runInfo, fileName, instrumentInfo, manufacturer, model, ionisation, analyzer, detector, header, peaksCount, peaks, get3Dmap
ExportClasses: mzR, mzRramp, mzRnetCDF

Package: ncdfFlow
Exports: ncfsUnlink, clone.ncdfFlowSet, read.ncdfFlowSet, NcdfFlowSetToFlowSet, as.flowSet
ExportMethods: show, [[, [, [[<-, colnames, parameters, compensate, rbind2, transform, ncfsApply, Subset, split, getIndices, updateIndices, initIndices, ncdfFlowSet, ncdfFlowSet_sync, ncdfFlowSet_open, addFrame, xyplot, densityplot, colnames<-, lapply, pData, pData<-, phenoData, length, sampleNames
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: 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

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: NormqPCR
Exports: geomMean, stabMeasureM, stabMeasureRho, selectHKs, deltaCt, deltaCq, replaceNAs, deltaDeltaCt, deltaDeltaCq, makeAllNAs, makeAllNewVal, combineTechReps, combineTechRepsWithSD, replaceAboveCutOff, CqValues, ComputeNRQs

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, clone, 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: oneChannelGUI
Exports: sapply, as.data.frame
ExportMethods: summary

Package: openCyto
Exports: .between_interval, cytokine, flowClust.1d, flowClust.2d, listgtMethods, mindensity, prior_flowClust, registerGatingFunction, registerPlugins, tailgate, templateGen
ExportMethods: show, ppMethod, plot, parameters, names, isCollapse, groupBy, getParent, getNodes, getGate, getChildren, gatingTemplate, gating, dims, alias
ExportClasses: ppMethod, 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, 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: 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: 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: 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: phyloseq
Exports: otuTable<-, sam_data<-, sample_data<-, sampleData<-, speciesAreRows<-, taxTab<-, tre<-, access, build_tax_table, distance, DPCoA, estimate_richness, export_env_file, 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, 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, plot_bar, plot_clusgap, plot_heatmap, 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_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, tipglom, topf, topk, topp, transform_sample_counts, transformSampleCounts, tre
ExportMethods: UniFrac, tip_glom, 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

Package: piano
Exports: loadMAdata, runQC, extractFactors, diffExp, polarPlot, loadGSC, runGSA, GSAsummaryTable, geneSetSummary, networkPlot, consensusScores, consensusHeatmap, runGSAhyper

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, day.infer.query, break.type.query, parse.buxco, parse.buxco.basic, add.labels.by.sample, adjust.labels, get.err.breaks, 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: 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: 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: markerSet, getPredictions, getMarkers, minClassScore, testMarkers, minMarkers, addMarkers, empPvalues, getStockcol, getStockpch, setStockcol, setStockpch, getUnknowncol, getUnknownpch, setUnknowncol, setUnknownpch, plot2D, addLegend, plotDist, 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
ExportMethods: chi2, show, MLearn, getWarnings, getSeed, getF1Scores, f1Count, levelPlot, plot
ExportClasses: GenRegRes

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: PSICQUIC
Exports: PSICQUIC, IDMapper, interactionTypes, detectionMethods, speciesIDs
ExportMethods: interactions, providers, rawQuery, addGeneInfo, show
ExportClasses: PSICQUIC, IDMapper

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
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: qpcrNorm
Exports: calcCV, ctQc, matrixByPlate, normQpcrHouseKeepingGenes, normQpcrQuantile, normQpcrRankInvariant, plotVarMean, readQpcr, readQpcrBatch, writeQpcr
ExportClasses: qpcrBatch

Package: qpgraph
Exports: qpHist, qpGraphDensity, qpCliqueNumber, qpClique, qpBoundary, qpGraph, qpAnyGraph, qpGetCliques, qpUpdateCliquesRemoving, qpIPF, qpHTF, qpPAC, qpPCC, qpRndGraph, qpRndWishart, qpG2Sigma, qpUnifRndAssociation, qpK2ParCor, qpPrecisionRecall, qpPRscoreThreshold, qpImportNrr, qpTopPairs, qpPlotNetwork, qpPlotMap, qpCov, qpRndHMGM, qpSampleFromHMGM, erGraphParam, dRegularGraphParam, erMarkedGraphParam, dRegularMarkedGraphParam, eQTLcrossParam
ExportMethods: qpNrr, qpAvgNrr, qpGenNrr, qpPAC, qpPCC, qpCItest, qpAllCItests, qpEdgeNrr, qpFunctionalCoherence, show, determinant, dim, dimnames, summary, rmvnorm, rcmvnorm, sim.cross, plot, rgraphBAM, UGgmm, HMgmm, rUGgmm, rHMgmm, $, eQTLcross, reQTLcross, addGenes, addeQTL, addGeneAssociation, alleQTL, ciseQTL, transeQTL
ExportClasses: SsdMatrix, erGraphParam, dRegularGraphParam, erMarkedGraphParam, dRegularMarkedGraphParam, UGgmm, HMgmm, eQTLcross, eQTLcrossParam

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: clearCheck, initDB, load_db, outlier.cutoff, outlier.norm, outlier.t, proportion.outliers.mle, proportion.outliers.robust, qaPreprocess, qoutlier, read.qaTask, rlm, save_db, saveToDB
ExportMethods: scatterPar, rFunc, queryStats, qpar, qaReport, qaCheck, plot, htmlReport, getQAStats, scatterPar<-, rFunc<-, qpar<-, htmlReport<-
ExportClasses: qaTask

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, qvalue.gui, 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: 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: 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: addBiochemicalReaction, addBiopaxInstance, addBiopaxInstances, addControl, addPathway, addPathwayComponents, addPhysicalEntity, addPhysicalEntityParticipant, addPropertiesToBiopaxInstance, calcGraphOverlap, CLASS_INHERITANCE_BP2, CLASS_INHERITANCE_BP3, CLASS_PROPERTIES_BP2, CLASS_PROPERTIES_BP3, colorGraphNodes, combineNodes, createBiopax, DATABASE_BIOPAX, 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: 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, setEmail, setCurrentSpecies, setCurrentGeneListPosition, setCurrentBackgroundPosition, setAnnotationCategories, popTotals, popHits, plot2D, percentages, membership, members, listTotals, is.connected, initialize, ids, getStub, getSpecieNames, getListName, getIdTypes, 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: enrichPathway, gseAnalyzer, 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, rederpost, rederexpresspost, att.setv, att.sete, att.mapv, att.mape, subg, cea, PluginBuilder, pluginParser
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, submitPlugin, deletePlugin, updatePlugins, dynwin
ExportClasses: RedPort, PluginBuilder

Package: REDseq
Exports: buildREmap, assignSeq2REsite, binom.test.REDseq, compareREDseq, distanceHistSeq2RE, summarizeByRE, plotCutDistribution, summarizeBySeq

Package: RefPlus
Exports: colMedians, normalize.quantiles2, rma.para, rmaplus, rmaref.predict

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: Resourcerer
Exports: resourcerer2BioC, getResourcerer

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: rhdf5
Exports: 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, H5Fclose, H5Fcreate, H5Fflush, H5Fopen, H5Gclose, H5Gcreate, H5Gcreate_anon, H5Gget_info, H5Gget_info_by_idx, H5Gget_info_by_name, H5Gopen, H5Iget_name, H5Iget_type, H5Iis_valid, 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, h5const, h5constType, h5createDataset, h5createFile, h5createGroup, h5createAttribute, h5default, h5dump, h5ls, h5read, 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
ExportClasses: H5IdComponent

Package: rHVDM
Exports: estimerrors, fitgene, HVDMcheck, HVDMreport, screening, training, training.nl, screening.nl, fitgene.nl, fitgene.lin, .exportfree, .importfree

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: RMAPPER
Exports: query, hits, readMAPPER, rmapperHelp, rmapperFactorTable
ExportMethods: hits, query
ExportClasses: mapperHits

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, 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, msmsWorkflow, multiply.formula, newMbWorkspace, newMsmsWorkspace, order.formula, parseMassBank, 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, 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: 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, 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: 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: RRHO
Exports: RRHO, pvalRRHO

Package: Rsamtools
Exports: path
ExportMethods: length, names, [, [[, show, getSeq, seqinfo, summarizeOverlaps, findSpliceOverlaps

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
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
ExportClasses: TNI, TNA

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, GFFFile, UCSCFile, BEDFile, WIGFile, ChainFile, FastaFile, GFF1File, GFF2File, GFF3File, BEDGraphFile, BED15File, GTFFile, GVFFile, BigWigFile, 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, 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
ExportClasses: RTLFile, CompressedFile, GFFFile, UCSCFile, BEDFile, WIGFile, ChainFile, FastaFile, GFF1File, GFF2File, GFF3File, BEDGraphFile, BED15File, GTFFile, GVFFile, BigWigFile, 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: 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: 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: SANTA
Exports: CheckAttributes, CreateGraph, CreateGrid, DistGraph, GraphDiffusion, GraphMFPT, Knet, Knode, MarkovCentrality, plot.Knet, SpreadHits

Package: SBMLR
Exports: readSBML, readSBMLR, saveSBML, saveSBMLR, sim, S4toS3

Package: SCAN.UPC
Exports: SCAN, SCANfast, UPC, UPCfast, SCAN_TwoColor, UPC_TwoColor, UPC_RNASeq, ParseMetaFromGtfFile, InstallBrainArrayPackage

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, .Last.lib
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: 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: shinyTANDEM
Exports: shinyTANDEM

Package: ShortRead
Exports: pData, phenoData, varLabels, varMetadata
ExportMethods: show, coerce, dim, length, [, [[, alphabetFrequency, alphabet, coverage, encoding, narrow, 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: 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: 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: 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: 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: 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, RNA.prepare.input

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: 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: 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, sNeighAny, sNeighDirect, sPipeline, sTopology, sTrainBatch, sTrainology, sTrainSeq, sWriteData, visColorbar, visColormap, visCompReorder, visDmatCluster, visHexComp, visHexGrid, visHexMapping, visHexMulComp, visHexPattern, visKernels, visVp

Package: sva
Exports: f.pvalue, irwsva.build, num.sv, sva, twostepsva.build, fsva, ComBat

Package: SwimR
Exports: createFrequencyMatrix, SwimR

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: 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, names, length, [, TCC, calcAUCValue, calcNormFactors, do_TbT, estimateDE, exactTestafterTbT, filterLowCountGenes, simulateReadCounts, getNormalizedData, getResult, MAplot, NBsample, plotFCPseudocolor, plot.TCC, WAD, ROKU
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, storeMatrix, getMatrixSet, getMatrixByID, getMatrixByName, deleteMatrixHavingID, initializeJASPARDB, ID, name, matrixClass, Matrix, bg, tags, matrixType, XMatrixList
ExportMethods: length, reverseComplement
ExportClasses: PFMatrix, PFMatrixList

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: 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: 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: 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

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: 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: UniProt.ws
Exports: cols, availableUniprotSpecies, lookupUniprotSpeciesFromTaxId
ExportMethods: keytypes, columns, keys, select, taxId, taxId<-, species

Package: VanillaICE
Exports: BeadStudioSet, robustSds, read.bsfiles, icePlatforms, copyNumberLimits, rowMAD, viterbi2Wrapper, rescale, hmm.setup, HmmOptionList, hmmSnpSet2, hmmBafLrrSet2, hmmBafLrrSetList2, hmmOligoSnpSet2
ExportMethods: hmm
ExportClasses: HmmOptionList

Package: VariantAnnotation
Exports: dbSNPFilter, regionFilter, VCF, VCFHeader, reference, header, 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, VRanges, VRangesList, asVCF, softFilter, resetFilter, totalDepth, altDepth, refDepth, sampleNames, sampleNames<-, altFraction, softFilterMatrix, softFilterMatrix<-, hardFilters, hardFilters<-, called, stackSamples, altDepth<-, refDepth<-, totalDepth<-, isIndel, probabilityToSnpMatrix, GLtoGP, readInfo, readGeno, readGT, tabulate
ExportMethods: filterVcf, scanVcf, scanVcfHeader, ScanVcfParam, readVcf, readVcfLongForm, writeVcf, expand, predictCoding, getTranscriptSeqs, refLocsToLocalLocs, MatrixToSnpMatrix, genotypeToSnpMatrix, snpSummary, locateVariants, summarizeVariants, fixed, fixed<-, ref, ref<-, alt, alt<-, qual, qual<-, filt, filt<-, info, info<-, geno, geno<-, strand, strand<-, [, [<-, cbind, rbind, mcols<-, genome, seqlevels, reference, samples, header, meta, keys, columns, select

Package: VariantTools
Exports: callVariants, qaVariants, tallyVariants, postFilterVariants, calculateConcordanceMatrix, callVariantConcordance, calculateVariantConcordance, VariantQAFilters, VariantCallingFilters, VariantTallyParam, VariantPostFilters, TallyVariantsParam, variantGR2Vcf, callSampleSpecificVariants, SampleSpecificVariantFilters, callWildtype, minCallableCoverage, matchVariants, %variant_in%, extractCoverageForPositions, makeVRangesFromVariantGRanges

Package: vbmp
Exports: vbmp, predictCPP, predError, predLik, predClass, covParams, plotDiagnostics

Package: Vega
Exports: vega, plotSegmentation

Package: VegaMC
Exports: vegaMC, sortData

Package: virtualArray
Exports: virtualArrayBuildExprs, virtualArrayBuildfData, virtualArrayBuildSampleInfo, virtualArrayComBat, virtualArrayCompile, virtualArrayDirs, virtualArrayExpressionSets, virtualArrayHclust, virtualArrayLoadRaw, virtualArrayMergeRecurse, normalize.ExpressionSet.gq, normalize.ExpressionSet.mrs, normalize.ExpressionSet.qd, normalize.ExpressionSet.nordi, normalize.ExpressionSet.mc

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: 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, subseq, subseq<-, xvcopy, compact, reverse
ExportMethods: subseq, subseq<-, xvcopy, compact, reverse, length, names, names<-, [, [<-, [[, [[<-, elementLengths, as.vector, as.integer, as.numeric, as.raw, as.data.frame, toString, coerce, c, show, showAsCell, width, compare, ==, !=, <=, duplicated, match, order, rank, is.unsorted, rev, endoapply, Views, slice, viewMins, viewMaxs, viewSums, viewMeans, viewWhichMins, viewWhichMaxs, updateObject
ExportClasses: SharedVector, SharedVector_Pool, SharedRaw, SharedRaw_Pool, SharedInteger, SharedDouble, XVector, XRaw, XInteger, XDouble, GroupedIRanges, XVectorList, XRawList, XIntegerViews

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