Package: ACME Exports: do.aGFF.calc, findRegions, read.resultsGFF, findClosestGene, write.sgr, getRefflat ExportMethods: show, print, plot, vals, threshold, cutpoints, chromosome, start, end ExportClasses: aGFF, aGFFCalc, ACMESet, ACMECalcSet Package: AffyCompatible ExportMethods: show 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: AffyTiling Exports: AnalyzeTilingCelFiles, TilingCelFiles2Probesets, AssociateWithGenes, AssociateWithInterval, parseBPMAP 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: AgiMicroRna Exports: readMicroRnaAFE, readTargets, qcPlots, boxplotMicroRna, plotDensityMicroRna, RleMicroRna, mvaMicroRna, mvaBASIC, hierclusMicroRna, HeatMapMicroRna, PCAplotMicroRna, cvArray, tgsMicroRna, tgsNormalization, rmaMicroRna, filterMicroRna, esetMicroRna, writeEset, basicLimma, getDecideTests, pvalHistogram, significantMicroRna Package: AnnotationDbi Exports: unlist2, showQCData, debugSQL, GOTerms, dbFileConnect, dbFileDisconnect, mergeToNamespaceAndExport, createAnnObjs.SchemaChoice, loadAnnDbPkgIndex, checkMAPCOUNTS, make_eg_to_go_map, make_go_to_eg_map, toSQLStringSet, populateDB, makeDBPackage, createSimpleBimap, available.db0pkgs, available.dbschemas, available.chipdbschemas, wrapBaseDBPackages, inpIDMapper, intraIDMapper, idConverter, summary, print.probetable, getProbeDataAffy, getProbeData_1lq, makeProbePackage 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, 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, makeAnnDbPkg ExportClasses: Bimap, FlatBimap, AnnObj, AnnDbObj, L2Rlink, AnnDbBimap, GoAnnDbBimap, Go3AnnDbBimap, GOTermsAnnDbBimap, AnnDbMap, IpiAnnDbMap, AgiAnnDbMap, ProbeAnnDbBimap, ProbeAnnDbMap, ProbeIpiAnnDbMap, ProbeGo3AnnDbBimap, GOTerms, AnnDbPkgSeed, GOFrame, GOAllFrame, KEGGFrame Package: ArrayExpress Exports: ArrayExpress, getAE, queryAE, magetab2bioc, getcolproc, getcolraw, procset, extract.zip 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, getContrast, getInteraction, getLevel, initialize, getCovariates, getDesign, getIntIndex, getTarget ExportClasses: regressResult, interactionResult, designMatrix, contrastMatrix Package: BCRANK Exports: bcrank, matchingSites ExportMethods: show, toptable, fname, searchPath, pwm, plot, bcrankScore, consensus, matchVector ExportClasses: BCRANKmatch, BCRANKsearch, BCRANKresult Package: BGmix Exports: BGmix, ccSummary, ccTrace, ccParams, ccPred, plotCompare, plotBasic, plotTrace, plotFDR, plotPredChecks, plotMixDensity, calcFDR, TailPP, histTailPP, FDRforTailPP, FDRplotTailPP, EstimatePi0, readBGX Package: BSgenome Exports: installed.genomes, available.genomes, BSgenome, installed.SNPs, available.SNPs, bsapply, GenomeData, GenomeDataList, gdreduce, organism, species, provider, providerVersion, releaseDate, releaseName, bsgenomeName, sourceUrl, SNPlocs_pkgname, SNPcount, SNPlocs, mseqnames, masknames, injectSNPs, getSeq, gdapply, gdApply, forgeSeqlengthsFile, forgeSeqFiles, forgeMasksFiles, forgeBSgenomeDataPkg ExportMethods: names, show, length, [[, $, score, matchPWM, countPWM, vmatchPattern, vcountPattern, organism, species, provider, providerVersion, releaseDate, releaseName, bsgenomeName, sourceUrl, SNPlocs_pkgname, SNPcount, SNPlocs, seqnames, seqlengths, mseqnames, masknames, injectSNPs, gdapply, forgeBSgenomeDataPkg ExportClasses: GenomeDescription, InjectSNPsHandler, BSgenome, GenomeData, GenomeDataList, BSgenomeDataPkgSeed Package: BUS Exports: BUS, pred.network, gene.similarity, gene.trait.similarity, gene.pvalue, gene.trait.pvalue Package: BayesPeak Exports: bayespeak, summarise.peaks, read.bed Package: BeadDataPackR Exports: decompressBeadData, compressBeadData Package: BicARE Exports: FLOC, bicluster, testAnnot, testSet, residue, makeReport 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: 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: Biobase Exports: Aggregate, addVigs2WinMenu, anyMissing, as.data.frame.ExpressionSet, assayDataNew, assayDataValidMembers, assayDataElementNames, assayDataElement, assayDataElementReplace, assayDataElement<-, biocReposList, cache, copyEnv, copySubstitute, getObjectSlots, createPackage, df2pD, dumpPackTxt, esApply, getPkgVigs, isUnique, l2e, listLen, matchpt, mkScalar, multiassign, note, openPDF, openVignette, package.version, reverseSplit, rowMax, rowMedians, rowMin, rowQ, read.exprSet, read.phenoData, read.pD, readExpressionSet, read.AnnotatedDataFrame, read.MIAME, selectSome, strbreak, subListExtract, testBioCConnection, lcSuffix, lcPrefix, lcPrefixC, updateOldESet, updateObjectFromSlots, userQuery, validMsg ExportMethods: [, [[, $, abstract, aggenv, aggfun, annotatedDataFrameFrom, annotation, channel, channelNames, coerce, combine, content, contents, description, dims, eList, experimentData, expinfo, exprs, featureNames, featureData, fData, fvarLabels, fvarMetadata, geneNames, getExpData, hybridizations, initfun, length, locked, makeDataPackage, normControls, notes, otherInfo, pData, phenoData, preproc, protocolData, sampleNames, samples, se.exprs, selectChannels, snpCall, snpCallProbability, storageMode, varLabels, varMetadata, annotation<-, description<-, dimLabels<-, eList<-, experimentData<-, exprs<-, featureNames<-, featureData<-, fData<-, fvarLabels<-, fvarMetadata<-, geneNames<-, notes<-, preproc<-, pData<-, phenoData<-, protocolData<-, sampleNames<-, snpCall<-, snpCallProbability<-, varLabels<-, varMetadata<-, assayData<-, se.exprs<-, storageMode<-, write.exprs, dim, dimLabels, assayData, reporterNames, reporterNames<-, pubMedIds, pubMedIds<-, isVersioned, isCurrent, classVersion, classVersion<-, updateObject, updateObjectTo, initialize, show, Compare ExportClasses: aggregator, container, eSet, phenoData, MIAME, characterORMIAME, annotatedDataset, AssayData, data.frameOrNULL, exprSet, 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: Biostrings Exports: IUPAC_CODE_MAP, mergeIUPACLetters, AMINO_ACID_CODE, GENETIC_CODE, RNA_GENETIC_CODE, DNA_BASES, RNA_BASES, DNA_ALPHABET, RNA_ALPHABET, AA_ALPHABET, xsbasetype, xsbasetype<-, alphabet, BString, DNAString, RNAString, AAString, compact, BStringSet, DNAStringSet, RNAStringSet, AAStringSet, unsplit.list.of.XStringSet, adjacentViews, XStringViews, unmasked, partitioning, BKeySortedData, DNAKeySortedData, RNAKeySortedData, AAKeySortedData, dataKey, dataTable, BKeySortedDataList, DNAKeySortedDataList, RNAKeySortedDataList, AAKeySortedDataList, xscat, BStringViews, readFASTA, writeFASTA, read.BStringSet, read.DNAStringSet, read.RNAStringSet, read.AAStringSet, fasta.info, fastq.geometry, write.XStringSet, save.XStringSet, read.XStringViews, write.XStringViews, FASTArecordsToCharacter, CharacterToFASTArecords, FASTArecordsToXStringViews, XStringSetToFASTArecords, letter, letterFrequencyInSlidingView, alphabetFrequency, hasOnlyBaseLetters, uniqueLetters, consensusMatrix, consensusString, mkAllStrings, oligonucleotideFrequency, dinucleotideFrequency, trinucleotideFrequency, nucleotideFrequencyAt, oligonucleotideTransitions, dinucleotideFrequencyTest, complement, reverseComplement, strrev, transcribe, cDNA, dna2rna, rna2dna, codons, translate, transcriptWidths, extractTranscripts, transcriptLocs2refLocs, toComplex, replaceLetterAt, .inplaceReplaceLetterAt, injectHardMask, N50, FASTArecordsToBStringViews, read.BStringViews, write.BStringViews, subXString, subBString, consmat, replaceLetterAtLoc, 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, WCPscoreStartingAt, matchWCP, countWCP, findPalindromes, findComplementedPalindromes, palindromeArmLength, complementedPalindromeArmLength, palindromeLeftArm, complementedPalindromeLeftArm, palindromeRightArm, complementedPalindromeRightArm, tb, tb.width, nnodes, hasAllFlinks, computeAllFlinks, patternFrequency, PDict, matchPDict, countPDict, whichPDict, vmatchPDict, vcountPDict, vwhichPDict, nmismatchStartingAt, nmismatchEndingAt, isMatching, matchDNAPattern, PWMscore, subpatterns, pattern, PhredQuality, SolexaQuality, quality, QualityScaledBStringSet, QualityScaledDNAStringSet, QualityScaledRNAStringSet, QualityScaledAAStringSet, insertion, deletion, unaligned, aligned, indel, nindel, PairwiseAlignedXStringSet, type, pid, PairwiseAlignedFixedSubject, nedit, mismatchTable, mismatchSummary, compareStrings, lcprefix, lcsuffix, pmatchPattern, lcsubstr, nucleotideSubstitutionMatrix, errorSubstitutionMatrices, qualitySubstitutionMatrices, pairwiseAlignment, stringDist, needwunsQS, basecontent, countbases, complementSeq, reverseSeq, revcompDNA, revcompRNA, longestConsecutive, matchprobes ExportMethods: length, [, rep, coerce, as.integer, as.numeric, as.character, as.matrix, toString, show, summary, start, end, width, Views, subpatterns, pattern, quality, insertion, deletion, unaligned, aligned, indel, nindel, type, score, pid, PairwiseAlignedXStringSet, PairwiseAlignedFixedSubject, mismatch, nmatch, nmismatch, nedit, mismatchTable, mismatchSummary, coverage, compareStrings, lcprefix, lcsuffix, pmatchPattern, lcsubstr, pairwiseAlignment, stringDist, needwunsQS, initialize, ls, length, names, names<-, show, [[, startIndex, endIndex, countIndex, unlist, neditStartingAt, neditEndingAt, isMatchingStartingAt, isMatchingEndingAt, mismatch, nmatch, nmismatch, coverage, matchPattern, countPattern, vcountPattern, matchLRPatterns, trimLRPatterns, matchProbePair, maxWeights, minWeights, maxScore, minScore, PWM, matchPWM, countPWM, matchWCP, countWCP, findPalindromes, findComplementedPalindromes, palindromeArmLength, complementedPalindromeArmLength, palindromeLeftArm, complementedPalindromeLeftArm, palindromeRightArm, complementedPalindromeRightArm, tb, tb.width, nnodes, hasAllFlinks, computeAllFlinks, head, tail, patternFrequency, PDict, matchPDict, countPDict, whichPDict, vmatchPDict, vcountPDict, vwhichPDict, length, names, [, [[, rep, show, ==, !=, duplicated, unique, is.unsorted, order, sort, rank, coerce, as.character, as.matrix, as.list, toString, toComplex, letter, substr, substring, letterFrequencyInSlidingView, alphabetFrequency, hasOnlyBaseLetters, uniqueLetters, consensusMatrix, consensusString, oligonucleotideFrequency, nucleotideFrequencyAt, dinucleotideFrequencyTest, chartr, reverse, complement, reverseComplement, codons, translate, replaceLetterAt, maskMotif, injectHardMask, as.complex, consmat, length, nchar, width, xsbasetype, xsbasetype<-, updateObject, compact, names, names<-, [, [[, [[<-, rep, append, union, intersect, setdiff, setequal, %in%, match, show, ==, !=, duplicated, unique, is.unsorted, order, sort, rank, coerce, as.character, unlist, as.matrix, as.list, toString, toComplex, narrow, subseq, threebands, subseq<-, collapse, gaps, Views, XStringViews, unmasked, maskedwidth, maskedratio, masks, masks<-, partitioning ExportClasses: XStringPartialMatches, XStringQuality, PhredQuality, SolexaQuality, QualityScaledXStringSet, QualityScaledBStringSet, QualityScaledDNAStringSet, QualityScaledRNAStringSet, QualityScaledAAStringSet, InDel, AlignedXStringSet0, AlignedXStringSet, QualityAlignedXStringSet, PairwiseAlignedXStringSet, PairwiseAlignedFixedSubject, PairwiseAlignedFixedSubjectSummary, MIndex, ByPos_MIndex, BOC_SubjectString, BOC2_SubjectString, PreprocessedTB, Twobit, ACtree2, PDict3Parts, PDict, TB_PDict, MTB_PDict, Expanded_TB_PDict, file, connection, XString, BString, DNAString, RNAString, AAString, XStringSet, BStringSet, DNAStringSet, RNAStringSet, AAStringSet, XStringViews, MaskedXString, MaskedBString, MaskedDNAString, MaskedRNAString, MaskedAAString, XStringSetList, BStringSetList, DNAStringSetList, RNAStringSetList, AAStringSetList, XKeySortedData, BKeySortedData, DNAKeySortedData, RNAKeySortedData, AAKeySortedData, XKeySortedDataList, BKeySortedDataList, DNAKeySortedDataList, RNAKeySortedDataList, AAKeySortedDataList, WCP, B_WCP, DNA_WCP, RNA_WCP, AA_WCP 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: CAMERA Exports: annotate, xsAnnotate, getPeaklist, getpspectra, annotateDiffreport ExportMethods: plotPsSpectrum, plotEICs, show, findAdducts, groupCorr, findIsotopes, groupFWHM ExportClasses: xsAnnotate Package: CGHbase Exports: cghRaw ExportMethods: initialize, plot.cghRaw, plot.cghSeg, plot.cghCall, plot.cghRegions, summaryPlot, 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: 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 ExportClasses: learningsets, cloutput, varseloutput, clvarseloutput, genesel, evaloutput, predoutput, tuningresult Package: CNTools Exports: diffBy, CNSeg ExportMethods: getRS, segBy, rs, genefilter, getCor, rs<-, getDist, segList<-, show, segList, madFilter ExportClasses: CNSeg, RS 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: Category Exports: .doHyperGTest, applyByCategory, cateGOry, cb_children, cb_contingency, cb_parse_band_Hs, cb_parse_band_Mm, cb_sigBands, cb_test, chrBandInciMat, ChrBandTreeFromGraph, DatPkgFactory, exampleLevels, findAMstats, geneGoHyperGeoTest, geneIds, geneIds<-, geneKeggHyperGeoTest, getPathNames, gseattperm, makeChrBandGraph, makeChrBandInciMat, 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, condGeneIdUniverse, testName, pvalueCutoff, pvalueCutoff<-, testDirection, testDirection<-, description, universeGeneIds, ontology, ontology<-, conditional, conditional<-, isConditional, 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: ChIPpeakAnno Exports: getAnnotation, annotatePeakInBatch, getAllPeakSequence, write2FASTA, getEnrichedGO, getUniqueGOidCount, hyperGtest, convert2EntrezID, addAncestors, BED2RangedData, GFF2RangedData, makeVennDiagram, findOverlappingPeaks 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: ChemmineR Exports: cmp.cluster, cmp.search, cmp.similarity, cmp.parse, cmp.parse1, sdf.subset, db.explain, cluster.sizestat, cluster.visualize, cmp.duplicated, sdf.visualize, db.subset Package: ChromHeatMap Exports: plotChrMap, makeChrStrandData, grabChrMapProbes, makeRangedDataList, createChrMatrix, chrHeatMap, drawMapDendro ExportMethods: chrNames ExportClasses: ChrStrandData, ChrStrandMatrix, ChrMapPlot Package: CoCiteStats Exports: actorAdjTable, gene.geneslist.sig, gene.geneslist.statistic, gene.gene.statistic, paperLen, twowayTable, twTStats Package: ConsensusClusterPlus Exports: ConsensusClusterPlus, calcICL Package: DEGseq Exports: DEGexp, DEGexp2, DEGseq, DEGseq.aln, DEGseq, getGeneExp, getGeneExp.aln, readGeneExp, samWrapper Package: DESeq Exports: newCountDataSet, counts, sizeFactors, sizeFactors<-, conditions, rawVarFunc, rawVarFuncTable, estimateSizeFactors, estimateVarianceFunctions, varianceFitDiagnosticsForMatrix, residualsEcdfPlotFromDiagnostics, varianceFitDiagnostics, residualsEcdfPlot, nbinomTest, getBaseMeansAndVariances, nbinomTest, estimateVarianceFunctionForMatrix, nbinomTestForMatrices, estimateSizeFactorsForMatrix, scvPlot, getVarianceStabilizedData, makeExampleCountDataSet, adjustScvForBias ExportClasses: CountDataSet Package: DFP Exports: discriminantFuzzyPattern, readCSV, plotMembershipFunctions, showDiscreteValues, showFuzzyPatterns, plotDiscriminantFuzzyPattern, calculateMembershipFunctions, discretizeExpressionValues, calculateFuzzyPatterns, calculateDiscriminantFuzzyPattern ExportMethods: show ExportClasses: ExpressionLevel, LowExpressionLevel, MediumExpressionLevel, HighExpressionLevel Package: DNAcopy Exports: CNA, exon.segment, segment, segments.p, segments.summary, smooth.CNA, glFrequency 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: EBImage Exports: Image, is.Image, as.Image, print.Image, Grayscale, TrueColor, Color, colorMode, colorMode<-, imageData, imageData<-, getNumberOfFrames, readImage, writeImage, display, animate, resize, rotate, flip, flop, translate, thresh, bwlabel, watershed, propagate, ocontour, paintObjects, rmObjects, reenumerate, median.Image, quantile.Image, normalize, filter2, blur, gblur, equalize, makeBrush, erode, dilate, opening, closing, distmap, floodFill, fillHull, rgbImage, channel, stackObjects, combine, tile, untile, drawfont, drawtext, getFeatures, hullFeatures, edgeProfile, edgeFeatures, moments, cmoments, smoments, rmoments, haralickMatrix, haralickFeatures, zernikeMoments ExportMethods: hist, show, Ops, [ ExportClasses: Image Package: ExpressionView Exports: LaunchEV ExportMethods: ExportEV, OrderEV 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, GDS Package: GEOsubmission Exports: microarray2soft Package: GGBase Exports: rsid, snpdepth, chrnum, probeId, snpsNear, smlSummary, MAFfilter, featureFilter, make_smlSet ExportMethods: chrnum, rsid, genesym, [, show, initialize, smList, smlEnv, probeId, snpLocs.Hs, exprs, [, plot_EvG, snpNames, getSnpLocs, phenoVar, plot_EvG2, combine, getAlleles, snps, coerce, updateObject ExportClasses: smlSet, snpLocs, gwSnpScreenResult, multiGwSnpScreenResult, cwSnpScreenResult, filteredGwSnpScreenResult, filteredMultiGwSnpScreenResult, chrnum, rsid, cnumOrMissing, genesym, probeId, phenoVar, filteredMultiGwSnpScreenResult, snpdepth, SessionInfo, smlSummary, multiCisTestResult Package: GGtools Exports: multffCT, makeCommonSNPs, checkCommonSNPs, diagffCC, maxchisq, cisSnpTests, geneRanges, snp130locs, bestCis, geneTrack ExportMethods: gwSnpTests, plot, topSnps, coerce, show, [, min_p_vals ExportClasses: multffManager, maxchisq Package: GOSemSim Exports: goSim, mgoSim, geneSim, mgeneSim, clusterSim, mclusterSim Package: GOstats Exports: combGOGraph, compCorrGraph, compGdist, enumPairs, GOGraph, GOLeaves, idx2dimnames, isTriad, makeGOGraph, notConn, oneGOGraph, reduce2Degreek, shortestPath, simLL, simLP, simUI, triadCensus, hyperGtable, hyperG2Affy, GOHyperG, probeSetSummary, termGraphs, inducedTermGraph, plotGOTermGraph, selectedGenes ExportMethods: hyperGTest, getGoGraph, pvalues, isConditional, description, oddsRatios, expectedCounts, htmlReport, goDag, geneCounts, universeCounts, geneIds, geneIdUniverse, condGeneIdUniverse, universeMappedCount, geneMappedCount, annotation, testName, summary ExportClasses: GOHyperGResult Package: GSEABase Exports: NullIdentifier, ENSEMBLIdentifier, EnzymeIdentifier, GenenameIdentifier, RefseqIdentifier, SymbolIdentifier, UnigeneIdentifier, EntrezIdentifier, AnnotationIdentifier, 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, EntrezIdentifier, UnigeneIdentifier, 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: gsri, gsriFromFile 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, geneAnswersConceptRelation, getConnectedGraph, getMultiLayerGraphIDs, getSingleLayerGraphIDs, getNextGOIDs, buildNet ExportMethods: getGeneInput, getTestType, getPValueT, getGenesInCategory, getGeneExprProfile, getAnnLib, getCategoryType, getEnrichmentInfo, setGeneInput, setTestType, setPValueT, setGeneExprProfile, setAnnLib, setCategoryType, setGenesInCategory, setEnrichmentInfo ExportClasses: GeneAnswers Package: GeneMeta Exports: CountPlot, dstar, f.Q, IDRplot, multExpFDR, mu.tau2, sigmad, tau2.DL, var.tau2, zScoreFDR, zScorePermuted, zScores ExportMethods: getdF Package: GeneR Exports: .seqSize, nSeq, .paramFromIndex, as.segSet, or.segSet, Xor.segSet, not.segSet, and.segSet, plot.segSet, as.data.frame.segSet, as.matrix.segSet, as.globalSeg, or.globalSeg, Xor.globalSeg, not.globalSeg, and.globalSeg, size.globalSeg, Length.globalSeg, Max.globalSeg, Min.globalSeg, as.matrix.globalSeg, plot.globalSeg, range.globalSeg, plot.profile, and.default, or.default, Xor.default, not.default, size.default, Min.default, Max.default, Length.default, insertSeq, strComp, strCompoSeq, placeString, revComp, getSeq, exactWord, dnaToRna, rnaToDna, assemble, concat, compoSeq, appendSeq, bankDensityProfile, densityProfile, freeSeq, freeAllSeq, sizeSeq, sliceSegment, seqSkew, GCcontent, setStrand, getStrand, setBegSeq, getBegSeq, setSeqSize, getSeqSize, getEndSeq, setAccn, getAccn, setParam, getParam, RtoA, AtoT, TtoA, RtoT, TtoR, AtoR, indexFasta, indexGbk, indexEmbl, makeIndex, deleteCR, posMaskedSeqFile, posMaskedSeq, upperSeq, lowerSeq, getOrfs, maxOrf, strTranslate, translate, showTable, readEmblLocation, readGbkLocation, readSeq, sizeSeqEmbl, sizeSeqGbk, sizeSeqFasta, fastaDescription, readFasta, readGbk, readEmbl, randomSeq, shuffleSeq, strReadEmbl, strReadGbk, strReadFasta, or, Xor, and, not, size, Min, Max, Length, .minimalSeg, relist, relistage, xorRecouvr, seqSrs, seqNcbi, writeEmblLine, writeEmblComment, writeEmblSeq, writeFasta, strWriteFasta, mask, unionSeg, bankSummary, readEmblDescript, .transf.limites, Match Package: GeneRegionScan Exports: exonStructure, findSequenceInGenome, getMetaprobesetsFromRegionOfInterest, getLocalMetaprobeIntensities, getServerProbeIntensities, getLocalProbeIntensities, getProbesetsFromRegionOfInterest, getProbesetsFromMetaprobeset ExportMethods: getSequence, translateSampleNames, plotOnGene, excludeDoubleMatchingProbes, addSnpPdata, geneRegionScan, plotCoexpression ExportClasses: ProbeLevelSet Package: GeneRfold Exports: fold, dotPlot, rnaPlot Package: GeneSelectMMD Exports: gsMMD, gsMMD.default, gsMMD2, gsMMD2.default, errRates, plotHistDensity 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: GeneticsBase Exports: LD, LDband, LDdist, as.geneSet, alleleCount, alleleLevels, alleles, alleleSummary, binsearch, callCodes, callCodes<-, carrier, convert, decodeCallCodes, description, description<-, desMarkers, diseq.inner, diseq.ci, dominant, ci.balance, errorMetrics, errorMetrics<-, extractAlleles, founderGeneSet, geneSet, genotypeFileFormats, genotypeLevels, genotypes, genotypeSummary, gregorius, haplo.score.w, haplo.score.slide.w, haplo.em.w, haplo.scan.w, head, HWE, HWE.chisq, HWE.exact, Armitage, Armitage.default, ArmitageTest, genotypeCoding, genotypeCoding.default, heterozygote, homozygote, html, html.GeneticsBaseSummary, html.markerSummary, html.LD, latex, latex.GeneticsBaseSummary, latex.markerSummary, latex.LD, LDView, left, makeMarkerInfo, makeTransTable, makeTransTableList, markerFileFormats, markerInfo, markerInfo<-, markerNames, markerSummary, missingCodes, missingCodes<-, nallele, nmarker, nobs, notes, notes<-, ped2geneSet, geneSet2Ped, PGtables, phase, phase<-, phenotypeFileFormats, ploidy, ploidy<-, print.GeneticsBaseSummary, print.markerSummary, read.fbat.phe, read.pbat.phe, read.phe, readGenes, readGenes.fbat.ped, readGenes.hapmap.ped, readGenes.pbat.ped, readGenes.ped, readGenes.perlegen, readGenes.pfizer, read.pfizer.Listing, read.pfizer.Pivot, recessive, right, sampleInfo, sampleInfo<-, studyInfo, studyInfo<-, summary.LD, tail, transTables, transTables<-, txt, txt.default ExportMethods: head, html, latex, left, plot, right, show, tail, LD, LDband, LDdist, [, [[, alleleCount, alleleLevels, alleles, callCodes, callCodes<-, carrier, description, description<-, dominant, errorMetrics, errorMetrics<-, genotypeLevels, genotypes, head, heterozygote, homozygote, HWE, markerInfo, markerInfo<-, markerNames, missingCodes, missingCodes<-, nallele, nmarker, nobs, notes, notes<-, phase, phase<-, ploidy, ploidy<-, plot, recessive, sampleInfo, sampleInfo<-, show, studyInfo, studyInfo<-, tail, transTables, transTables<- ExportClasses: LD, LDband, LDdist, geneSet 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: 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 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: GenomicFeatures Exports: transcripts_deprecated, exons_deprecated, introns_deprecated, extractTranscriptsFromGenome, makeTranscriptDb, supportedUCSCtables, makeTranscriptDbFromUCSC, makeTranscriptDbFromBiomart, saveFeatures, loadFeatures, as.list, transcripts, exons, cds, transcriptsByOverlaps, exonsByOverlaps, cdsByOverlaps, id2name, transcriptsBy, exonsBy, cdsBy, intronsByTranscript, fiveUTRsByTranscript, threeUTRsByTranscript ExportMethods: seqnames, seqlengths, show, as.list ExportClasses: GenomicFeatures, TranscriptDb Package: GenomicRanges Exports: seqnames, seqnames<-, seqlengths, seqlengths<-, strand, strand<-, GRanges, GRangesList, validCigar, cigarOpTable, cigarToQWidth, cigarToWidth, cigarQNarrow, cigarNarrow, cigarToIRanges, cigarToIRangesListByAlignment, cigarToIRangesListByRName, queryLoc2refLoc, queryLocs2refLocs, splitCigar, cigarToRleList, cigarToCigarTable, summarizeCigarTable, rname, rname<-, cigar, qwidth, grglist, grg, rglist, qnarrow, readGappedAlignments, GappedAlignments ExportMethods: length, names, names<-, coerce, as.data.frame, unlist, seqnames, ranges, strand, seqlengths, elementMetadata, seqnames<-, ranges<-, strand<-, seqlengths<-, elementMetadata<-, start, end, width, start<-, end<-, width<-, [, [<-, c, rev, seqselect, seqselect<-, split, window, flank, resize, shift, disjoin, gaps, range, reduce, coverage, union, intersect, setdiff, punion, pintersect, psetdiff, findOverlaps, countOverlaps, match, %in%, show, rname, rname<-, cigar, qwidth, grglist, grg, rglist, qnarrow ExportClasses: GRanges, GRangesList, GappedAlignments 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: GlobalAncova Exports: GAGO, GAKEGG, GABroad, GlobalAncova.decomp, pair.compare, Plot.sequential, Plot.all ExportMethods: GlobalAncova, GlobalAncova.closed, Plot.genes, Plot.subjects Package: GraphAlignment Exports: LinearAssignment, ComputeM, AlignNetworks, CreateScoreMatrix, InvertPermutation, Permute, Trace, InitialAlignment, GetBinNumber, VectorToBin, MatrixToBin, ComputeScores, GenerateExample, ComputeLinkParameters, ComputeNodeParameters, EncodeDirectedGraph, AnalyzeAlignment, AlignedPairs, .Last.lib Package: HELP Exports: readSampleKey ExportMethods: calcGC, calcPrototype, calcTm, combineData, createWiggle, exprs2, exprs2<-, fuzzyMatches, getFeatures, getSamples, plotBins, plotChip, plotFeature, plotPairs, quantileNormalize, readDesign, readPairs Package: HTqPCR Exports: cbind.qPCRset, changeCtLayout, clusterCt, featureCategory, featureCategory<-, featureClass, featureClass<-, featurePos, featurePos<-, featureType, featureType<-, filterCategory, filterCtData, flag, flag<-, getCt, getCtHistory, heatmapSig, limmaCtData, mannwhitneyCtData, n.samples, n.wells, normalizeCtData, plotCtBoxes, plotCtCategory, plotCtCor, plotCtDensity, plotCtHeatmap, plotCtHistogram, plotCtOverview, plotCtPCA, plotCtReps, plotCtRQ, plotCtScatter, plotCtSignificance, plotCVBoxes, plotCtLines, plotCtCard, rbind.qPCRset, readCtData, setCategory, setCt<-, summary, ttestCtData, plotCtPairs ExportMethods: [, exprs, exprs<-, featureNames, featureNames<-, sampleNames, sampleNames<-, show, summary ExportClasses: qPCRset Package: HilbertVis Exports: hilbertCurve, hilbertCurvePoint, plotHilbertCurve, shrinkVector, plotLongVector, makeWiggleVector, hilbertImage, makeRandomTestData, showHilbertImage Package: HilbertVisGUI Exports: simpleLinPlot, hilbertDisplay, hilbertDisplayThreeChannel, dotsapply Package: IRanges Exports: setValidity2, new2, isTRUEorFALSE, isSingleInteger, isSingleNumber, isSingleString, isSingleIntegerOrNA, isSingleNumberOrNA, isSingleStringOrNA, isConstant, normargShift, normargWeight, safeExplode, strsplitAsListOfIntegerVectors, svn.time, solveUserSEW0, IRanges, solveUserSEW, successiveIRanges, whichAsIRanges, asNormalIRanges, H2LGrouping, Dups, PartitioningByEnd, PartitioningByWidth, Binning, RangedData, RangedDataList, RangedSelection, FilterRules, RDApplyParams, RangesList, IRangesList, RleViewsList, MaskCollection.show_frame, Mask, read.gapMask, read.agpMask, read.liftMask, read.rmMask, read.trfMask, SharedVector.compare, SharedVector.copy, SharedRaw, SharedRaw.readInts, SharedRaw.writeInts, SharedRaw.read, SharedRaw.write, SharedRaw.readComplexes, XRaw, XInteger, XDouble, XNumeric, newViews, successiveViews, SimpleList, DataFrame, LogicalList, IntegerList, NumericList, ComplexList, CharacterList, RawList, RleList, DataFrameList, SplitDataFrameList, coverage.normargWidth, endoapply, mendoapply, seqapply, mseqapply, tseqapply, seqsplit, elementType, elementLengths, metadata, elementMetadata, metadata<-, elementMetadata<-, seqselect, seqselect<-, mapply, Map, isEmpty, width, mid, start<-, width<-, end<-, shift, restrict, narrow, resize, threebands, reduce, gaps, findOverlaps, overlap, countOverlaps, countOverlap, subsetByOverlaps, nearest, precede, follow, reflect, flank, punion, pintersect, psetdiff, pgap, disjoin, disjointBins, Rle, runLength, runValue, nrun, runLength<-, runValue<-, shiftApply, findRange, findRun, paste, nobj, grouplength, members, vmembers, togroup, togrouplength, high2low, low2high, grouprank, togrouprank, ngap, as.env, isNormal, isDisjoint, whichFirstNotNormal, IntervalTree, xvcopy, reverse, coverage, nir_list, active, active<-, maskedwidth, maskedratio, collapse, ranges, ranges<-, subseq, subseq<-, subject, Views, subviews, trim, slice, values, values<-, columnMetadata, columnMetadata<-, runmean, runsum, runwtsum, runq, viewApply, viewMins, viewMaxs, viewSums, viewMeans, viewWhichMins, viewWhichMaxs, viewRangeMins, viewRangeMaxs, cbind, rbind, table, xtabs, rangedData, rangedData<-, applyFun, applyFun<-, applyParams, applyParams<-, simplify, simplify<-, filterRules, filterRules<-, reducerFun, reducerFun<-, reducerParams, reducerParams<-, rdapply, universe, universe<-, space, score, score<-, matchMatrix, queryHits, subjectHits ExportMethods: lapply, sapply, tapply, [, [<-, [[, [[<-, $, ==, !=, <=, >=, <, >, Ops, Math, Math2, Summary, Complex, coerce, show, summary, length, length<-, names, names<-, nrow, NROW, ncol, NCOL, dim, rownames, colnames, dimnames, rownames<-, colnames<-, dimnames<-, duplicated, unique, order, sort, rank, is.unsorted, rev, rep, rep.int, head, tail, start, end, min, max, range, pmax, pmin, pmax.int, pmin.int, 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<-, nlevels, 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, toString, unlist, stack, update, append, !, which, c, union, intersect, setdiff, split, splitRanges, eval, with, within, t, is.na, na.omit, na.exclude, complete.cases, %in%, by, match, Reduce, Filter, Find, Position, updateObject, endoapply, mendoapply, seqselect, seqselect<-, mapply, Map, isEmpty, width, start<-, width<-, end<-, isNormal, isDisjoint, whichFirstNotNormal, shift, restrict, narrow, resize, threebands, reduce, gaps, punion, pintersect, psetdiff, xvcopy, reverse, coverage, nobj, grouplength, members, vmembers, togroup, togrouplength, high2low, low2high, grouprank, togrouprank, ngap, nir_list, active, active<-, desc, desc<-, maskedwidth, maskedratio, collapse, subseq, subseq<-, subject, Views, subviews, trim, Rle, runLength, runValue, nrun, runLength<-, runValue<-, shiftApply, findRange, runmean, runsum, runwtsum, runq, viewApply, viewMins, viewMaxs, viewSums, viewMeans, viewWhichMins, viewWhichMaxs ExportClasses: characterORNULL, Annotated, Sequence, DataTable, DataTableORNULL, SimpleList, CompressedList, Ranges, RangesORmissing, IRanges, NormalIRanges, IntervalTree, Grouping, H2LGrouping, Dups, Partitioning, PartitioningByEnd, PartitioningByWidth, Binning, SharedVector, SharedVector_Pool, SharedRaw, SharedRaw_Pool, SharedInteger, SharedDouble, Views, XVector, XRaw, XInteger, XDouble, GroupedIRanges, XVectorList, XRawList, XIntegerViews, 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, RleViewsList, SimpleRleViewsList, DataFrame, DataFrameList, SimpleDataFrameList, SplitDataFrameList, CompressedSplitDataFrameList, SimpleSplitDataFrameList, RangedData, RangedDataList, FilterRules, RDApplyParams, RangesMatching, RangedSelection Package: ITALICS Exports: ITALICS, analyseCGH, getQuartet, getResidu, getCorrection, getEffet, getConfDat, getModel, readQuartetCopyNb, getSnpInfo, fromSnpToQuartet, fromQuartetToSnp, addInfo, trainITALICS Package: Icens Exports: Bisect, BVcliques, BVclmat, BVmacprod, BVsupport, EM, EMICM, EMICMmac, Intersection, ISDM, Maclist, Macmat, MLEintvl, PGM, Plotboxes, PMGA, rescaleP, Subset, VEM, VEMICMmac 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: KEGGSOAP Exports: color.pathway.by.objects, get.best.best.neighbors.by.gene, getBestNeighbors, get.best.neighbors.by.gene, get.compounds.by.pathway, get.enzymes.by.pathway, get.genes.by.motifs, get.genes.by.organism, get.genes.by.pathway, get.motifs.by.gene, get.paralogs.by.gene, get.pathways.by.compounds, get.pathways.by.enzymes, get.pathways.by.genes, get.pathways.by.reactions, get.reactions.by.pathway, list.databases, list.organisms, list.pathways, mark.pathway.by.objects, search.compounds.by.name, search.glycans.by.name, search.compounds.by.composition, search.glycans.by.composition, search.glycans.by.mass, search.compounds.by.mass, search.compounds.by.subcomp, search.glycans.by.kcam, bget, bconv Package: KEGGgraph ExportMethods: getDisplayName, getEntryID, getKEGGID, getKEGGgeneLink, getType, getName, getSubtype, getValue, getTitle, getComponent, getPathwayInfo, getReactions, getKEGGgeneLink, subtypeDisplay, getSubstrate, getProduct, show, nodes, edges, nodes<- ExportClasses: KEGGEdge, KEGGGroup, KEGGNode, KEGGPathwayInfo, KEGGReaction, KEGGEdgeSubType, KEGGGraphics, KEGGPathway, KEGGPathwayInfo Package: LBE Exports: LBEa, LBEplot, LBE, LBEsummary, LBEwrite Package: LMGene Exports: genediff, glog, LMGene, lnorm, lnormeS, neweS, norm, psmeans, plotMeanSD, rowaov, tranest, tranestAffyProbeLevel, transeS 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: LiquidAssociation ExportMethods: CNM.full, CNM.simple, getsGLA, getsLA, GLA, LA, plotGLA 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: MEDME ExportMethods: initialize, chr, pos, logR, smoothed, AMS, RMS, CG, org, [, show ExportClasses: MEDMEset 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, xvalSpec, getVarImp, balKfold.xvspec, rdacvI, rdacvML, rdaI, rdaML, plotXvalRDA, makeLearnerSchema, standardMLIConverter, sldaI, fs.absT, fs.probT, ksvmI, knn.cvI, knn.cv2, adaI, fs.topVariance, hclustI, kmeansI, pamI, blackboostI, gbm2, BgbmI ExportMethods: show, RObject, confuMat, MLearn, planarPlot, Predict, getVarImp, plot, trainPredictions, testScores, testPredictions, fsHistory, report, getDist, getConverter ExportClasses: varImpStruct, classifierOutput, learnerSchema, xvalSpec, clusteringOutput 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: 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: MeasurementError.cor Exports: cor.me.vector, cor.me.matrix 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: Mfuzz Exports: acore, cselection, cselection, fill.NA, filter.NA, filter.std, filter.std, kmeans2, kmeans2.plot, mfuzz, mfuzz.plot, mfuzz.plot2, Mfuzzgui, mfuzzColorBar, overlap, overlap.plot, partcoef, randomise, standardise, standardise2, top.count Package: MiChip Exports: parseRawData, outputAnnotatedDataMatrix, returnAnnotatedDataMatrix, removeUnwantedRows, standardRemoveRows, myForgivingMedian, setIntensityCutoff, correctForFlags, summarizeIntensitiesAsMedian, normalizePerChipMedian, boxplotData, boxplotDataNoFile, plotIntensitiesScatter, workedExampleMedianNormalize, workedExampleNotNormalizedData Package: MotIV Exports: motifMatch, exportAsTransfacFile, generateDBScores, readDBScores, writeDBScores, getGademPWM, readGademPWMFile, readPWMfile, viewAlignments, summary, plot, split, filter, combine, makePWM, setFilter, combine, trimPWMedge, exportAsRangedData, similarity, viewMotifs, occurences, cooccurences, getPWM, nMotifs ExportMethods: show, summary, combine, filter, split ExportClasses: motiv, matches, alignments, transcriptionFactor, filter 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: OutlierD Exports: OutlierD 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: 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: PGSEA Exports: .rwb ExportClasses: smc Package: PICS Exports: paraPriorTF, paraEMTF ExportMethods: show, summary, plot, density, chromosome, score, se, seF, seR, sigmaSqF, sigmaSqR, mu, delta, w, code, length, K, [, [[ ExportClasses: segReads, segReadsList, pics, picsError, picsList 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: PROMISE Exports: PROMISE, avg.abs.genestat, jung.rstat, spearman.rstat, promise.genestat 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: 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: 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 Package: ROC Exports: AUC, AUCi, dxrule.sca, pAUC, pAUCi, ROC, rocdemo.sca, trapezint ExportMethods: plot, points, lines ExportClasses: rocc Package: RPA Exports: get.probe.noise.estimates, rpa, RPA.dcost, rpa2eset, RPA.iteration, rpa.plot, RPA.pointestimate, RPA.preprocess, set.priors ExportMethods: [, [[, show ExportClasses: rpa, rpa.list, rpa.priors 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: RTools4TB Exports: createSignatures4TB, DBFMCL, getData4DBFMCL, doRankTransformation, DBF, MCL, doNormalScore, writeDBFMCLresult, clusterEisen, heatmapFromCDT, colorScale, plotGeneExpProfiles, matplotProfiles, getSignatures, getExpressionMatrix, getTBInfo, createGraph4BioC ExportClasses: DBFMCLresult 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: Rdbi Exports: dbAppendTable, dbClearResult, dbColumnInfo, dbConnect, dbConnectionInfo, dbDisconnect, dbGetQuery, dbGetResult, dbListTables, dbReadTable, dbReconnect, dbResultInfo, dbSendQuery, dbWriteTable, double.quote, expand.asis, .Last.lib, list.to.csv, list.to.key.pair.string, printListPairs, single.quote, strip.line.feeds Package: RdbiPgSQL Exports: make.db.names, PgSQL, psql, rpgsql.cast.values, rpgsql.cast.values.1042, rpgsql.cast.values.1043, rpgsql.cast.values.1082, rpgsql.cast.values.1083, rpgsql.cast.values.25, rpgsql.cast.values.default, rpgsql.data.type, rpgsql.data.type.dates, rpgsql.data.type.default, rpgsql.data.type.times, rpgsql.format.values, rpgsql.format.values.dates, rpgsql.format.values.default, rpgsql.format.values.times, dbAppendTable Package: Rdisop Exports: addMolecules, decomposeIsotopes, decomposeMass, getMass, getFormula, getIsotope, getValid, getMolecule, getScore, initializeCHNOPS, initializeCHNOPSMgKCaFe, initializeCHNOPSNaK, initializeElements, initializePSE, initializeCharges, isotopeScore, RcppVersion, subMolecules Package: RefPlus Exports: colMedians, normalize.quantiles2, rma.para, rmaplus, rmaref.predict Package: Resourcerer Exports: resourcerer2BioC, getResourcerer Package: Rgraphviz Exports: agopen, agread, agwrite, buildEdgeList, buildNodeList, checkAttrs, drawAgNode, drawTxtLabel, getDefaultAttrs, getNodeLabels, getNodeNames, graphvizVersion, graphLayout, makeNodeAttrs, pieGlyph, removedEdges, toFile, agopenSimple, 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, 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: Ringo Exports: autocor, chipAlongChrom1, corPlot, 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 ExportMethods: get, ls, initialize, plot, show, image, arrayName, chromosomeNames, genome, probes, arrayName<-, genome<-, update, cellType, cellType<-, nonzero, cbind2 ExportClasses: probeAnno, cher, qop 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: RmiR ExportClasses: miRtcList 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: Rredland Exports: openRedlWorld, readRDF, restoreBDB, cleanXSDT, getArcsWith, getObjectProperties, getDatatypeProperties, getOWLClasses, getPropertyRange, getOWLProperties, getPropertiesWithDomain, getClassElements, getClassGraph, getOWLSubclasses, nodeFromURIString, world ExportMethods: ref, freeRedl, getStatus, setStatus, makeRedlURI, show, size, coerce, world ExportClasses: redlWorld, redlModel, redlURI, redlNode Package: Rsamtools ExportMethods: length, names, [, [[, show ExportClasses: ScanBamParam, BamViews 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: Ruuid Exports: getuuid ExportMethods: show, as.character, ==, !=, uuid ExportClasses: Ruuid, uuidt 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: SBMLR Exports: readSBML, readSBMLR, saveSBML, saveSBMLR, simulate 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: SLGI Exports: gi2Interactome, getInteraction, getSharedInteraction, hyperG, comemberIn, congruence, normInteraction, topInteraction, createSquareMatrix, byComplex, domainDist, getSharedDomains, sharedBy, getUniquePairs, getTestedPairs, seqMatcherAlign, getAlignStats, twoWayTable, modelSLGI, getFASTAname, test2Interact, iSummary, withinComplex, sharedInt ExportMethods: plot, compare, show ExportClasses: siResult 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: SNPchip Exports: centromere, chromosomeSize, integer2chromosome, plotPredictions, showSummary, plotCytoband ExportMethods: $, $<-, plotSnp, snpPar, snpPar<-, initialize, coerce, dbSnpId, fragmentLength, hmmPredict, plot, show, smoothSnp, summary, updateObject, snpset ExportClasses: ParESet, ParSnpCopyNumberSet, ParSnpCallSet, ParSnpSet Package: SPIA Exports: spia, plotP Package: SSPA Exports: pilotData, sampleSize, Power, plotEffectSize ExportMethods: plot, hist, show 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: ShortRead Exports: pData, phenoData, varLabels, varMetadata ExportMethods: show, coerce, dim, length, [, [[, alphabetFrequency, alphabet, coverage, narrow, strand, trimLRPatterns, width, append, rbind, %in% Package: SpeCond Exports: getDefaultParameter, createParameterMatrix, fitPrior, fitNoPriorWithExclusion, getSpecificResult, getSpecificOutliersStep1, SpeCond, getMatrixFromExpressionSet, getProfile, writeSpeCondResult, writeUniqueProfileSpecificResult, writeGeneResult, getFullHtmlSpeCondResult, getGeneHtmlPage 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 Package: TargetSearch Exports: FAMEoutliers, FindPeaks, medianRILib, Profile, sampleRI, ImportLibrary, ImportLibrary.tab, ImportLibrary.msp, ImportSamples, ImportSamplesFromDir, ImportFameSettings, NetCDFPeakFinding, peakCDFextraction, peakFind, plotFAME, plotRIdev, plotAllRIdev, plotPeak, plotSpectra, plotAllSpectra, quantMatrix, ProfileCleanUp, RIcorrect, rt2ri, ri2rt, Write.Results, writeMSP, baseline, baselineCorrection, fixRIcorrection, TargetSearchGUI 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<-, show ExportClasses: tsLib, tsRim, tsSample, tsMSdata, tsProfile 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: VanillaICE Exports: hmm, hmm.setup, robustSds 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: adSplit Exports: adSplit, diana2means, drawRandomPS, randomDiana2means, makeEID2PROBESenv Package: affy Exports: .setAffyOptions ExportMethods: show, exprs, featureNames, geneNames, sampleNames, se.exprs, updateObject ExportClasses: AffyBatch Package: affyContam Exports: setCircRegion, setRectRegion, getCircRegion, getRectRegion Package: affyPLM ExportClasses: PLMset 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: 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: affycoretools Exports: limma2annaffy, foldFilt, vennSelect, vennCounts2, plotma, probes2table, affystart, plotDeg, plotHist, plotPCA, convert.back, hyperG2annaffy, vennSelectBM, limma2biomaRt, linksBM, annBM, foldFiltBM, probes2tableBM, vennSelectFC, hyperGoutput, getUniqueLL, genefilter, filterfun, kOverA, pOverA, cv 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, genelocator, 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, neighborGeneFinder, 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 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: apComplex Exports: bhmaxSubgraph, findComplexes, mergeComplexes, plotComplex, sortComplexes 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, addXYfromGAL, aqm.plot, aqm.boxplot, aqm.maplot, aqm.density, aqm.probesmap, aqm.meansd, aqm.heatmap, aqm.pca, aqm.rle, aqm.nuse, aqm.rnadeg, aqm.qcstats, aqm.pmmm, aqm.prepdata, aqm.prepaffy, aqm.spatial, aqm.spatialbg, aqm.writereport ExportClasses: aqmobj.box, aqmobj.pmmm, aqmobj.rnadeg, aqmobj.dens, aqmobj.prepaffy, aqmobj.spatial, aqmobj.pca, aqmobj.heat, aqmobj.prepdata, aqmobj.spatialbg, aqmobj.ma, aqmobj.probesmap, aqmobj.msd, aqmobj.qcs, aqmobj.nuse, aqmobj.rle Package: baySeq ExportMethods: dim, [, show ExportClasses: countData Package: beadarray Exports: SAMSummary, BeadChipSummary, medianNormalise, rankInvariantNormalise, plotBeadIntensities, plotBeadLocations, imageplot, plotMAXY, plotMA, plotRG, plotXY, plotOnSAM, readQC, readIllumina, readBeadSummaryData, findBeadStatus, boxplotBeads, createBeadSummaryData, findAllOutliers, qcBeadLevel, plotBeadDensities, beadResids, readBGX, normaliseIllumina, setWeights, beadarrayUsersGuide, addArrayMask, removeArrayMask, clearArrayMask, showArrayMask, BASH, BASHCompact, BASHDiffuse, BASHExtended, generateE, generateNeighbours, BGFilter, BGFilterWeighted, chooseClusters, closeImage, denseRegions, viewBeads, getAnnotation, setAnnotation, getControlAnno, calculateDetection, calculateBeadLevelScores, probePairsPlot, lmhPlot, backgroundControlPlot, poscontPlot, gradientPlot, outlierPlot, HULK, HULKResids, readTIFF, plotTIFF, readLocs ExportMethods: initialize, show, se.exprs, exprs, [, [[, $, phenoData, pData, sampleNames, samples, se.exprs<-, exprs<-, NoBeads<-, Detection<-, QCInfo<-, dim, assayData, initialize, NoBeads, Detection, backgroundCorrect, QCInfo, copyBeadLevelList, combineBeadLevelLists, getProbeIntensities, getArrayData, arrayNames, numBeads, getVariance, combine ExportClasses: ExpressionSetIllumina, BeadLevelList 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<-, geneNames<-, pData<-, phenoData<-, sampleNames<-, assayData<-, featureData<-, fData, fData<-, dim, assayData, reporterNames, initialize, arrayType<-, arrayID<-, arrayType, arrayID, plotQC, reportSamplePanelQC, calculateGSR, cn.segments, cn.segments<- ExportClasses: SnpSetIllumina, SnpSetSegments, QCIllumina 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: bgx Exports: bgx, standalone.bgx, readOutput.bgx, plotExpressionDensity, plotDEDensity, plotDEHistogram, rankByDE, plotDiffRank 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: biocDatasets Exports: createProbeCoords, randomDNASequences, tilingIRanges, msubseq, randomIRanges, tilingProbes, expression_arraywide, replicate_arraywide Package: biocGraph Exports: imageMap Package: biocViews Exports: writeBiocViews, getBiocViews, write_VIEWS, write_REPOSITORY, genReposControlFiles, extractVignettes, extractManuals, writeRepositoryHtml, writePackageDetailHtml, getSubTerms, getBiocSubViews, writeTopLevelView, writeHtmlDoc, write_SYMBOLS ExportMethods: coerce, show, htmlDoc, htmlValue, htmlFilename ExportClasses: Htmlized, PackageDetail, pdAuthorMaintainerInfo, pdVignetteInfo, pdDownloadInfo, pdDetailsInfo, pdDescriptionInfo, pdVigsAndDownloads, RepositoryDetail, rdPackageTable, BiocView, bvTitle, bvPackageTable, bvSubViews, bvParentViews Package: biomaRt Exports: listMarts, getGene, getSequence, exportFASTA, useMart, listDatasets, useDataset, listAttributes, listFilters, getBM, getXML, getLDS, attributePages, filterOptions, filterType, getBMlist, getGO, attributeSummary, martDisconnect, NP2009code ExportMethods: show ExportClasses: Mart Package: bridge Exports: bridge.2samples, bridge.3samples 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, configurationAsScreenPlot, convertOldCellHTS, convertWellCoordinates, getEnVisionRawData, getEnVisionCrosstalkCorrectedData, getDynamicRange, getMeasureRepAgreement, getTopTable, getSettings, getZfactor, gseaModule, imageScreen, normalizePlates, plotSpatialEffects, readPlateList, readHTAnalystData, 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: cghMCR Exports: cghMCR, plot.DNAcopy, MCR, mergeMCRProbes, SGOL ExportMethods: gol, plot ExportClasses: cghMCR, SGOL Package: charm Exports: bgAdjust, countGC, cpgdensity, dmrFdr, dmrFinder, getControlIndex, methPercent, methp, normalizeBetweenSamples, normalizeWithinSamples, plotDensity, qcReport, readCharm, spatialAdjust, validatePd, pmindex, bgindex Package: chipseq Exports: contextDistribution, diffPeakSummary, chipseqFilter, readReads, extendReads, copyIRanges, copyIRangesbyChr, laneSubsample, combineLanes, islandDepthPlot, coverageplot, sparse.density, basesCovered, densityCorr, estimate.mean.fraglen, subsetSummary, peakCutoff, peakSummary ExportMethods: estimate.mean.fraglen Package: clippda Exports: sampleClusteredData, negativeIntensitiesCorrection ExportMethods: show ExportClasses: aclinicalProteomicsData Package: clusterStab ExportMethods: ecdf, hist, benhur, clusterComp ExportClasses: BenHur, ClusterComp Package: codelink Exports: readCodelink, writeCodelink, reportCodelink, plotMA, plotCorrelation, plotDensities, plotCV, imageCodelink, bkgdCorrect, normalize, mergeArray, createWeights, arrayNew, selCV, cutCV, fc2Cond, na2false, logCodelink, readCodelinkSet ExportMethods: [, show, summary, summaryFlag, annotation, codCorrect, codNormalize, codPreprocess, probeNames, probeTypes, getSNR, getInt, getBkg, getInfo, meanSNR, codPlot, exprs, chipDevice, filterSNR, codUniverse, writeCluster, writeCodelink, averageProbes ExportClasses: Codelink, CodelinkSet, CodelinkSetUnique Package: copa Exports: copa, plotCopa, copaPerm, tableCopa, scatterPlotCopa, summaryCopa Package: cosmo Exports: cosmo, bgModel, bfile2tmat, makeConSet, addCon, makeBoundCon, makePalCon, makeShapeCon, makeShapeDiffCon, makePosFreqCon, makeSubMotifCon, writeConFile, readConFile, rseq, simScore, license.cosmo ExportMethods: plot, summary, print, show ExportClasses: align, intInfo, cosmo, constraintSet, boundCon, palCon, posFreqCon, shapeCon, shapeDiffCon, subMotifCon Package: cosmoGUI Exports: constraintBuilder Package: crlmm Exports: crlmm, crlmmCopynumber, crlmmIllumina, genotype, readIdatFiles, snprma, snprma2, crlmm2, genotype2, batch, crlmmCopynumber2 ExportMethods: open, [, show, lM, copyNumber ExportClasses: CNSetLM, ffdf, list Package: ctc Exports: hc2Newick, hclust2treeview, r2cdt, r2atr, r2gtr, r2cluster, r2xcluster, read.eisen, xcluster, xcluster2r Package: cycle Exports: ar1analysis, backgroundData, fdrfourier, fourierscore Package: ddCt Exports: barploterrbar, ddCtAbsolute, elist, elistWrite, errBarchart, SDMFrame, CSVFrame, readSDM, ColMap, replaceVectorByEquality, write.htmltable, writeSimpleTabCsv ExportMethods: coreData, coreData<-, rightCensoring, fileNames, sampleNames, sampleNames<-, uniqueDetectorNames, uniqueDetectorNames<-, uniqueSampleNames, uniqueSampleNames<-, detectorNames<-, detectorNames, replaceDetector, replaceSample, removeDetector, removeSample, level, levelErr, Ct, CtErr, dCt, dCtErr, ddCt, ddCtErr, numberCt, numberNA, ddCtExpression, errBarchart, InputFrame ExportClasses: ddCtExpression, InputFrame, InputReader, SDMReader, CSVReader, ColMap Package: domainsignatures Exports: dataSource, getKEGGdata, gseDomain, getKEGGdescription ExportMethods: show ExportClasses: ipDataSource Package: dualKS Exports: dksTrain, dksWeights, dksSelectGenes, dksClassify, dksPerm, KS, dksCustomClass ExportMethods: plot, show, summary ExportClasses: DKSGeneScores, DKSClassifier, DKSPredicted Package: ecolitk Exports: arrowsArc, chromPos2angle, cPlotCircle, ecoli.len, gccontent, linesArc, linesChrom, linesCircle, linkedmultiget, pointsArc, polar2xy, polygonArc, polygonChrom, polygonDisk, rotate, wstringapply, xy2polar Package: edd Exports: eddDistList, T3, U01, N01, LN01, B82, CS1, B28, centerScale, dmixnorm, edd, eddObsolete, flatQQNorm, flatQQNormY, fq.matrows, latEDtable, makeCandmat.raw, makeCandmat.theor, maxKSp, mkt, plotED, pmixnorm, qmixnorm, rmixnorm, rmixnorm.alt, MIXN1 ExportMethods: CDFname, genName, latexTag, Mad, med, parms, plotlim, qfName, qfun, stub, tag, testVec ExportClasses: eddDist Package: edgeR ExportMethods: show ExportClasses: DGEList, deDGEList, EBList, TopTags 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 ExportMethods: coerce, summary, htmlReport, pvalues, geneCounts, oddsRatios, expectedCounts, universeCounts, universeMappedCount, geneMappedCount, geneIdUniverse, condGeneIdUniverse, 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: exonmap ExportMethods: fc, tt ExportClasses: PC Package: externalVector Exports: externalCharacter, externalComplex, externalInteger, externalLogical, externalMatrix, externalNumeric, externalVector, makeSlice, nonSlotAttributes, nonSlotAttributes<-, rebind, setExternalStorageClass, setVirtualMethod, SubscriptList ExportMethods: allNA, allocatedSize, allocatedType, allocate, allocator, anyNA, apply, Arith, as.character, as.complex, as.data.frame, asEach, as.integer, as.list, as.logical, as.matrix, as.numeric, as.Rmatrix, as.Rvector, as.single, as.vector, [<-, [, [[<-, [[, c, coerce, colMeans, colSums, Compare, Complex, cor, cov2cor, cov, deallocate, defaultElement, dim<-, dim, dimnames<-, dimnames, external.size<-, external.size, force, getExternalStorage, getNativeStorageMethods, getPointer, initialize, initializeResource, internalType, is.finite, is.infinite, is.na, is.nan, lapply, length<-, length, log, match, Math, mean, median, names<-, names, Ops, reinitializePointer, rowMeans, rowSums, sapply, setDimNames, setNames, show, Subset2, Subset, Summary, var ExportClasses: noneIndex, allIndex, externalAllocator, externalResource, externalStorage, externalVector, externalVectorWithStorage, gcAllocator, indirectExternalMatrix, indirectExternalVector, matrixIndex, NAIndex, nativeStorageMethods, nativeStorageMethodsList, positiveIndex, simpleStorage, sliceIndex, vectorIndex Package: factDesign Exports: contrastTest, findFC, kRepsOverA, madOutPair, outlierPair, par2lambda Package: fbat Exports: readPed, readLink, readHapMap, getFounders, fbat, fbat.default, pedHardyWeinberg, pedHardyWeinberg.default, pedFlagHomo, pedFlagHomo.default, pedGFreq, pedGFreq.default, pedAFreq, pedAFreq.default, viewHW, viewstat, viewFlagHomo, summaryPvalue, checkMarkers, checkMarkers.default, checkMendelian, checkMendelian.default, missGFreq, missGFreq.default Package: flagme ExportMethods: show, plot ExportClasses: peaksDataset Package: flowClust ExportMethods: show, summary, plot, density, hist, filter, %in%, [, [[, length, coerce, coerce<-, Subset, split, ruleOutliers, ruleOutliers<-, Map, criterion, criterion<- ExportClasses: flowClust, flowClustList, tmixFilter, tmixFilterResult, tmixFilterResultList Package: flowCore Exports: action, actions, add, alias, arcsinhTransform, asinht, as.data.frame.manyFilterResult, assign, biexponentialTransform, boundaryFilter, char2ExpressionFilter, cleanup, colnames, colnames<-, compensate, compensatedParameter, compensateView, compensateActionItem, compensation, curv1Filter, curv2Filter, Data, dg1polynomial, each_col, each_row, EHtrans, ellipsoidGate, eval, exponential, expressionFilter, fcActionReference, fcAliasReference, fcCompensateReference, fcDataReference, fcFilterReference, fcFilterResultReference, fcNormalizationReference, fcReference, fcSubsettingReference, fcTransformReference, fcTreeReference, fcViewReference, filter, filterDetails, filterDetails<-, filterList, filterReference, filterSet, flowFrame, flowSet, fsApply, gate, gateActionItem, gateView, get, head, hyperlog, identifier, identifier<-, invsplitscale, isFCSfile, isNull, journal, kmeansFilter, keyword, keyword<-, linearTransform, lnTransform, logarithm, logTransform, logicleTransform, inverseLogicleTransform, ls, manyFilterResult, mget, norm2Filter, ncol, nodes, normalization, normalizeActionItem, normalizeView, nrow, fcNullReference, parameters, parameters<-, parent, polygonGate, polytopeGate, print, quadGate, quadratic, quadraticTransform, ratio, read.FCS, read.FCSheader, read.flowSet, rectangleGate, Rm, sampleFilter, scaleTransform, sinht, sort, spillover, split, splitscale, splitScaleTransform, squareroot, Subset, subsettingActionItem, subsetting, summarizeFilter, summary, tail, timeFilter, toTable, truncateTransform, transformActionItem, transformList, transformReference, transformView, tree, undo, unitytransform, view, views, workFlow, write.FCS, write.flowSet, %&%, %in%, %subset%, %on% ExportMethods: action, actions, add, alias, assign, c, cbind2, coerce, colnames, colnames<-, compensate, Data, description, description<-, dim, each_row, each_col, exprs, exprs<-, featureNames, filter, filterDetails, filterDetails<-, filterReference, fsApply, gate, get, 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, 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, filterReference, filterResult, filterResultList, filterSet, filterSummary, filterSummaryList, flowFrame, flowSet, gateActionItem, gateView, hyperlog, intersectFilter, invsplitscale, kmeansFilter, logarithm, logicalFilterResult, manyFilterResult, multipleFilterResult, normalization, normalizeActionItem, normalizeView, norm2Filter, parameters, parameterTransform, parameterFilter, polygonGate, polytopeGate, quadGate, quadratic, randomFilterResult, ratio, rectangleGate, sampleFilter, setOperationFilter, sinht, splitscale, squareroot, subsetFilter, subsettingActionItem, subsetting, timeFilter, transform, transformActionItem, transformFilter, transformMap, transformList, transformReference, transformView, unionFilter, unitytransform, view, workFlow 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: flowFlowJo Exports: readFlowJoList, getFlowJoGates, collectSummaryFlowInfo, getFlowJoSummary, createFlowReport, simplifyGateNames, flowJoCompensate, getWellId ExportClasses: flowJoObj, flowJoList, fcsSummary, fcsSummaryList Package: flowMeans Exports: flowMeans, changepointDetection, plot, summary, show Package: flowMerge Exports: fitPiecewiseLinreg, pFlowMerge, checkForRemoteErrors, flowObj, ENT, NENT, BIC, ICL, split, map ExportMethods: getData, merge, plot, summary, show, split ExportClasses: flowClust, flowMerge, flowObj 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: flowStats Exports: lymphGate, lymphFilter, oneDGate, quadrantGate, rangeGate, warpSet, proBin, binByRef, gaussNorm, plotBins, calcPearsonChi, calcPBChiSquare, gpaSet, iProcrustes, normQA ExportMethods: %in% ExportClasses: lymphFilter Package: flowTrans Exports: flowTrans, extractParams, summary.flowTransResult ExportMethods: flowTrans Package: flowUtils Exports: read.gatingML, testGatingCompliance Package: flowViz Exports: addName, flowViz.par.set, flowViz.par.get, glines, gpoints, glpoints, glpolygon, gpolygon, hexbin, 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: frma Exports: frma, barcode ExportMethods: initialize, se.exprs, weights, residuals, as.ExpressionSet ExportClasses: frmaExpressionSet Package: frmaTools Exports: makeVectors, makeVectorPackage, convertPlatform, hgu133plus2ASaFrma, hgu133a2ASaFrma Package: gaga Exports: checkfit, checkfit.gagafit, classpred, classpred.gagafit, dcgamma, findgenes, findgenes.gagafit, fitGG, geneclus, geneclus.gagafit, getpar, getpar.gagafit, mcgamma, parest, parest.gagafit, posmeansGG, posmeansGG.gagafit, print.gagaclus, print.gagafit, print.gagahyp, rcgamma, simGG, simnewsamples, simnewsamples.gagafit, powclasspred, powclasspred.gagafit Package: gaggle Exports: gaggleInit, getNameList, getCluster, getMatrix, getNetwork, getTuple, broadcast, geese, getTargetGoose, setTargetGoose, setSpecies, getSpecies, showGoose, hideGoose, testGagglePackage, connectToGaggle, disconnectFromGaggle 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: gene2pathway Exports: retrain, retrain.signaltrans, gene2pathway, gene2pathway.signaltrans, getComponents, get.elements.by.pathway, color.pathway.by.elements, ORF2Entrez, Entrez2ORF, test.overrepresentation 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: 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: Makesense, imageMap ExportClasses: file, connection Package: genoCN Exports: code.genotype, genoCNA, genoCNV, plotCN Package: genomeIntervals Exports: readGff3, parseGffAttributes, getGffAttribute ExportMethods: annotation, annotation<-, seq_name, seq_name<-, strand, strand<-, inter_base, inter_base<-, type<-, [, [[, $, coerce, size, show, core_annotated, interval_union, interval_complement, interval_intersection, interval_overlap, distance_to_nearest ExportClasses: Genome_intervals, Genome_intervals_stranded Package: genomes ExportClasses: genomes Package: girafe Exports: AlignedGenomeIntervals, plotAligned, trimAdapter, perWindow, fracOverlap, intPhred, coverageOneStrand, addNBSignificance, plotNegBinomFit, clusters, coerce, organism, plot ExportMethods: plot, [, interval_overlap, interval_included, chromosome, coerce, coverage, clusters, detail, export, extend, matches, matches<-, organism, organism<-, reads, reads<-, reduce, score, score<-, seq_name, show, strand, strand<-, subset, width, which_nearest ExportClasses: AlignedGenomeIntervals Package: globaltest Exports: globaltest, gt, permutations, sampling, geneplot, sampleplot, regressionplot, checkerboard, gt.multtest, mlogit, gtGO, combine, leafNodes, draw, gtKEGG, gtBroad, comparative, focusLevel, inheritance, covariates, features, subjects, gt.options, findFocus, getFocus, makeGOstructure ExportMethods: [, [[, show, result, p.value, length, names, names<-, sort, size, hist, z.score, scale, plot, fit, summary, residuals, fitted.values, coefficients, genesets, alias, alias<-, model.matrix, weights, p.adjust, subsets ExportClasses: gt.result, gt.barplot, mlogit, gt.object, GOstructure 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 Package: gpls Exports: gpls, glpls1a, glpls1a.cv.error, glpls1a.train.test.error, glpls1a.mlogit, glpls1a.logit.all, glpls1a.mlogit.cv.error Package: graph Exports: 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, extractFromTo, subsetEdgeSets, extractGraphAM 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, removeEdge, removeNode, show, subGraph, threshold, toGXL, union, validateGXL, coerce, toDotR, attrDefaults, attrDefaults<-, edgeDataDefaults, edgeDataDefaults<-, nodeDataDefaults, nodeDataDefaults<-, edgeData, edgeData<-, nodeData, nodeData<-, attrDataItem, attrDataItem<-, removeAttrDataItem<-, ugraph, leaves, updateGraph, extractFromTo ExportClasses: distGraph, clusterGraph, graph, graphNEL, file, connection, gzfile, bzfile, url, graphAM, attrData, simpleEdge, edgeSet, edgeSetNEL, edgeSetAM, multiGraph, renderInfo, MultiGraph, graphBAM Package: hexbin Exports: erode, erode.hexbin, getHMedian, gplot.hexbin, grid.hexagons, grid.hexlegend, hboxplot, hcell2xy, hexbin, hexcoords, hexList, hexpolygon, hexViewport, hexVP.abline, plotMAhex, hexVP.loess, hexMA.loess, hsmooth, list2hexList, pushHexport, smooth.hexbin, hdiffplot, hcell2xyInt, hgridcent, hexGraphPaper, hexTapply, optShape, inout.hex, BTC, BTY, LinGray, LinOCS, heat.ob, magent, plinrain, hexbinplot, hexplom, panel.hexbinplot, panel.hexplom, panel.hexboxplot, panel.hexgrid, panel.hexloess, hexlegendGrob ExportMethods: erode, hsmooth, plot, summary, show, coerce ExportClasses: hexbin, erodebin, smoothbin, hexVP, integer or NULL, hexbinList 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: 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: iChip Exports: iChip1, iChip2, enrichreg, lmtstat Package: iFlow Exports: iflow, guiEnv Package: idiogram Exports: .usedChromExprs, .rwb ExportClasses: cytoband Package: impute Exports: impute.knn Package: iterativeBMA Exports: BssWssFast, bma.predict, brier.score, imageplot.iterate.bma, iterateBMAglm.train, iterateBMAglm.train.predict, iterateBMAglm.train.predict.test, iterateBMAglm.wrapper Package: keggorthology Exports: getKOprobes, indRender, keggDF2graph, getKOtags Package: lapmix Exports: lapmix.Fit, laptopTable, lap.volcanoplot Package: limma ExportMethods: show ExportClasses: RGList, MAList, EListRaw, EList, MArrayLM, TestResults, LargeDataObject Package: logicFS Exports: getMatEval, logic.bagging, logic.oob, logic.pimp, logicFS, make.snp.dummy, minDNF, prime.implicants, 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.permInput, vim.permSNP, vim.permSet Package: logitT Exports: logitTAffy Package: lumi Exports: IlluminaID2nuID, addControlData2lumi, addNuID2lumi, addNuId2lumi, affyExpresso, affyVstRma, 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, plotControlData, plotHousekeepingGene, plotSampleRelation, plotStringencyGene, plotVST, probeID2nuID, produceGEOPlatformFile, produceGEOSampleInfoTemplate, produceGEOSubmissionFile, rsn, seq2id, ssn, targetID2nuID, vst, rankinvariant ExportMethods: beadNum, beadNum<-, boxplot, combine, density, detection, detection<-, getHistory, hist, MAplot, plotCDF, pairs, plot, sampleNames, se.exprs, se.exprs<-, show, summary, [ ExportClasses: LumiBatch Package: mBPCR Exports: logAdd, indexLA0, estGlobParam, computeLA0Vect, computeA10, computeRecursions, computeRegrCurve, computePCReg, computeMBPCR, writeEstProfile, importCNData, estProfileWithMBPCR, estProfileWithMBPCRforOligoSnpSet, plotEstProfile Package: maSigPro Exports: average.rows, get.siggenes, i.rank, make.design.matrix, maSigPro, p.vector, PlotGroups, PlotProfiles, position, reg.coeffs, see.genes, stepback, stepfor, suma2Venn, T.fit, two.ways.stepback, two.ways.stepfor 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: 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, pretty.dend, 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: 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<-, maGb<-, maRb<-, 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, maSpotCol, maControls, maNsamples, maGnames, maTargets, maA, maMloc, maMscale, maControls, maNormCall, boxplot, image, points, text, lines, summary, maNotes, show, [ ExportClasses: marrayInfo, marrayLayout, marrayRaw, marrayNorm, ShowLargeObject Package: matchprobes Exports: combineAffyBatch Package: mdqc Exports: mdqc, prcomp.robust Package: metaArray Exports: poe.mcmc, poe.em, intcor 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: methVisual Exports: plotAbsMethyl, MethLollipops, heatMapMeth, matrixSNP, plotMatrixSNP, methCA, methFisherTest, methWhitneyUTest, cgInAlign, findNonAligned, Cooccurrence, MethAlignNW, cgMethFinder, makeDataMethGFF, MethDataInput, selectRefSeq, readBisulfFASTA, makeLocalExpDir, makeTabFilePath, MethylQC, coversionGenom Package: methylumi Exports: methylumiR, extractBarcodeAndPosition, normalizeMethyLumiSet, getAssayDataNameSubstitutions ExportMethods: getHistory, betas, pvals, exprs, summary, show, combine, hist, boxplot, pairs, [, QCdata, plotSampleIntensities, qcplot, methylated, unmethylated, unmethylated<-, methylated<-, QCdata<-, exprs<-, pvals<-, betas<-, controlTypes, corplot ExportClasses: MethyLumiSet, MethyLumiQC, MethyLumi Package: miRNApath ExportMethods: show ExportClasses: mirnapath Package: microRNA Exports: get_selfhyb_subseq, show_selfhyb_counts, show_selfhyb_lengths, seedRegions, matchSeeds, RNA2DNA 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: 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, 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, quicknem Package: nnNorm Exports: maNormNN, detectSpatialBias, compNorm Package: occugene Exports: checkFormat, delta0, eMult, etDelta, fCumul, fFit, occup2Negenes, unbiasB0, unbiasDelta0, varMult Package: oligo Exports: basecontent, cleanPlatformName, read.celfiles, read.xysfiles, sequenceDesignMatrix, list.xysfiles, readSummaries, getCrlmmSummaries, getNgsColorsInfo, read.xysfiles2, read.celfiles2, basicRMA, darkColors, seqColors, getAffinitySplineCoefficients, getBaseProfile, crlmm, snprma, justSNPRMA, justCRLMM, getPD, plotM ExportMethods: backgroundCorrect, normalize, summarize, normalizeToTarget, boxplot, bg, bg<-, bgSequence, db, exprs, getContainer, getPlatformDesign, getX, getY, hist, image, MAplot, mm, mm<-, mmindex, mmSequence, pm, pm<-, pmChr, pmAllele, pmindex, pmFragmentLength, pmOffset, pmPosition, pmSequence, pmStrand, probeNames, rma Package: oligoClasses Exports: pdPkgFromBioC, requireAnnotation, affyPlatforms, celfileDate, list.celfiles, is.ffmatrix, isPackageLoaded, ldStatus, ldSetOptions, parStatus, ocProbesets, ocSamples, ldPath, getBar, createFF, setCluster, delCluster, getCluster, requireClusterPkgSet, requireClusterPkg, ocLapply, splitIndicesByLength, splitIndicesByNode, initializeBigMatrix, initializeBigVector, chromosome2integer, annotationPackages, addFeatureAnnotation ExportMethods: 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<-, db, isSnp, position, sampleNames, CA, CB, CA<-, CB<-, A, B, A<-, B<- ExportClasses: AlleleSet, oligoSnpSet, SnpSuperSet, CNSet, ExpressionFeatureSet, SnpFeatureSet, SnpCnvFeatureSet, TilingFeatureSet, ExonFeatureSet, GeneFeatureSet, DBPDInfo, ExpressionPDInfo, FeatureSet, TilingPDInfo, AffyTilingPDInfo, AffyExpressionPDInfo, AffySNPPDInfo, AffySNPCNVPDInfo, AffyGenePDInfo, AffyExonPDInfo, NgsExpressionPDInfo, NgsTilingPDInfo Package: oneChannelGUI Exports: summary, sapply, as.data.frame Package: pamr Exports: pamr.adaptthresh, pamr.batchadjust, pamr.confusion, pamr.cv, pamr.fdr, pamr.from.excel, pamr.decorrelate, pamr.geneplot, pamr.knnimpute, pamr.knnimpute.old, pamr.listgenes, pamr.makeclasses, pamr.menu, pamr.cube.root, pamr.indeterminate, pamr.pairscore, pamr.plotcen, pamr.plotcvprob, pamr.plotcv, pamr.plotfdr, pamr.predictmany, pamr.predict, pamr.score.to.class1, pamr.score.to.class2, pamr.surv.to.class2, pamr.confusion.survival, pamr.plotsurvival, pamr.plotstrata, pamr.pvalue.survival, pamr.to.excel, pamr.train, print.pamrtrained, print.pamrcved, pamr.test.errors.surv.compute, pamr.xl.compute.offset, pamr.xl.error.trace, pamr.xl.get.offset, pamr.xl.derive.adjusted.prior, pamr.xl.get.default.training.parameters, pamr.xl.get.uniform.prior, pamr.xl.get.sample.prior, pamr.xl.get.class.names, pamr.xl.get.class.labels, pamr.xl.get.number.of.classes, pamr.xl.process.data, pamr.xl.compute.cv.confusion, pamr.xl.compute.confusion, pamr.xl.is.a.subset, pamr.xl.listgenes.compute, pamr.xl.plot.test.probs.compute, pamr.xl.plot.training.error.compute, pamr.xl.plotcen.compute, pamr.xl.plotcv.compute, pamr.xl.plotcvprob.compute, pamr.xl.predict.test.class, pamr.xl.predict.test.class.only, pamr.xl.predict.test.probs, pamr.xl.test.data.impute, pamr.xl.test.errors.surv.compute, pamr.xl.test.errors.compute, pamr.xl.transform.class.labels, pamr.xl.transform.data, pamr.xl.transform.test.data, pamr.xl.plotsurvival, pamr.xl.plotsurvival.test, pamr.xl.predict.test.surv.class, pamr.xl.plotsurvival.strata, pamr.xl.test.get.soft.classes, pamr.xl.get.threshold.range, pamr.xl.get.soft.class.labels Package: parody Exports: calout.detect, mv.calout.detect, hamp.scale.3, tukeyor, box.scale Package: pathRender Exports: rendercMAPPathway, graphcMAP, pwayRendAttrs, reduceES, plotExGraph, colorNodes ExportMethods: plot ExportClasses: pwayGraph, coloredGraph Package: pcaMethods Exports: bpca, checkData, scores.pcaRes, loadings.pcaRes, dim.pcaRes, kEstimateFast, kEstimate, llsImpute, RnipalsPca, nipalsPca, nlpca, listPcaMethods, pca, nni, asExprSet, plotPcs, showPcaRes, showNniRes, biplot.pcaRes, predict.pcaRes, residuals.pcaRes, fitted.pcaRes, plot.pcaRes, plotR2, svdPca, ppca, prep, robustPca, robustSvd, svdImpute, Q2 ExportMethods: slplot, fitted, resid, residuals, predict, summary, show, print, R2cum, scl, scaled, sDev, wasna, nmissing, method, completeObs, center, centered, nVar, nObs, nPcs, cvstat, nP, DModX, leverage ExportClasses: nniRes, pcaRes, nlpcaNet Package: pcot2 Exports: aveExprs, aveProbe, corplot2, corplot, Cor, geneLocator, getImat, pco, pcot2, plotCor, rb, rg, t2.permu, t2, t2.unequ, wb 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: pint Exports: iterative.window, fixed.window, fit.dependency.model, ppca, pcca, pcca.isotropic, pfa, fit.cgh.mrna.byname, fit.cgh.mir.byname, plot.DependencyModel, plot.ChromosomeArmModels, plot.ChromosomeModels, plot.GenomeModels, screen.cgh.mrna, screen.cgh.mir, z.expectation, z.effects, W.effects, pint.data, pint.match ExportMethods: [[, [[<-, setLoc<-, setGeneName<-, setArm<-, setChromosome<-, getW, getPhi, getScore, getLoc, getGeneName, getChromosome, getArm, getModelMethod, getParams, getPArm, getQArm, getWindowSize, getModelNumbers, topGenes, topModels, orderGenes, findModel ExportClasses: DependencyModel, ChromosomeArmModels, 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: 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 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: qpcrNorm Exports: calcCV, ctQc, matrixByPlate, normQpcrHouseKeepingGenes, normQpcrQuantile, normQpcrRankInvariant, plotVarMean, readQpcr, readQpcrBatch, writeQpcr ExportClasses: qpcrBatch Package: qpgraph Exports: qpHist, qpGraphDensity, qpCliqueNumber, qpClique, qpGraph, qpAnyGraph, qpGetCliques, qpIPF, qpPAC, qpPCC, qpRndGraph, qpRndWishart, qpG2Sigma, qpK2ParCor, qpPrecisionRecall, qpPRscoreThreshold, qpImportNrr, qpFunctionalCoherence ExportMethods: qpNrr, qpAvgNrr, qpPAC, qpPCC, qpCItest, qpEdgeNrr Package: quantsmooth Exports: quantsmooth, quantsmooth.seg, quantsmooth.cv, getLambdaMin, plotSmoothed, getChangedRegions, getChangedIdx, numericCHR, characterCHR, scaleto, plotChromosome, prepareGenomePlot, paintCytobands, lengthChromosome, drawSimpleChrom, position2Cytoband, grid.chromosome Package: rGADEM Exports: GADEM ExportMethods: length, dim, names, consensus, parameters, viewPWM, startPos, endPos, nOccurrences, nMotifs, plot, getPWM ExportClasses: parameters, align, gadem, motif Package: rHVDM Exports: estimerrors, fitgene, HVDMcheck, HVDMreport, screening, training, training.nl, screening.nl, fitgene.nl, fitgene.lin, .exportfree, .importfree Package: rMAT ExportMethods: show, summary, rbind ExportClasses: tilingSet Package: rama Exports: arrange.row, est.shift, fit.model, is.row.na, ls.effect, mat.mean, ratio.plot, weight.plot Package: rbsurv Exports: rbsurv, rbsurv.default Package: rflowcyt Exports: ContourScatterPlot, standard, boxplot.FCS, plotdensity.FCS, plotECDF.FCS, plotvar.FCS, parallelCoordinates, ImageParCoord, read.FCS, read.series.FCS, convertS3toS4, make.grid, make.density, pairs.CSP, legend.CSP, metaData, percentile.FCS, PercentPos.FCS, ProbBin.FCS, breakpoints.ProbBin, createGate, emp.f, extractGateHistory, extractGatedData, fcs.type.facscan256, get.h, get.num.modes, get.p, pkci2.flowcytest, summary.ProbBin.FCS, runflowcytests, plot2sets.FCS, plotQA.FCS, MODE, icreateGate, showgate.FCS, JointImageParCoord, plot.ProbBin.FCS, KS.flowcytest, WLR.flowcytest, ROC.FCS, rect.box.idx ExportMethods: print, show, summary, plot, fluors, addParameter, checkvars, coerce, dim.FCS, equals, fixvars ExportClasses: FCS, FCSmetadata, FCSsummary, FCSgate Package: rtracklayer Exports: genomeBrowsers, start, end, strand, start<-, end<-, ranges, GenomicRanges, GenomicData, GenomicSelection, IRanges, RangedDataList, score, score<-, as.data.frame, ucscGenomes, export.bw, import.bw, BigWigSelection 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, import, import.bed, import.bed15, import.bedGraph, import.gff, import.gff1, import.gff2, import.gff3, import.ucsc, import.wig, sequence<-, track<-, track, trackNames, trackNames<-, getTable, tableNames, trackName, trackName<-, tableName, tableName<-, ucscTrackModes, ucscTrackModes<-, coerce, initialize, show, [, ucscTableQuery, genome, genome<-, chrom, chrom<-, range, range<-, visible, visible<-, start, end, start<-, end<-, score, score<-, as.data.frame, strand ExportClasses: connection, file, url, gzfile, unz, pipe, sockconn, characterORconnection, BrowserSession, BrowserView, UCSCSession, UCSCView, UCSCData, TrackLine, BasicTrackLine, GraphTrackLine, Bed15TrackLine, UCSCTrackModes, BigWigSelection Package: safe Exports: error.FDR.BH, error.FDR.YB, error.FWER.Bonf, error.FWER.Holm, error.FWER.WY, gene.results, getAnnotateOptions, getCmatrix, getErrorNames, getGlobalStatisticNames, getLocalStatisticNames, getPImatrix, getResamplingOptions, getSAFEResults, global.AveDiff, global.Fisher, global.Kolmogorov, global.Pearson, global.Wilcoxon, local.f.ANOVA, local.t.LM, local.t.paired, local.t.Student, local.t.Welch, local.z.COXPH, safedag, safeplot, safe Package: segmentSeq ExportMethods: dim, [, show ExportClasses: segData, alignmentData Package: seqLogo Exports: seqLogo, makePWM ExportMethods: plot, summary, print, show ExportClasses: pwm Package: siggenes Exports: args.ebam, args.finda0, args.sam, ebam, ebam2excel, ebam2html, filterALL, 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 ExportMethods: show, print, plot, summary, identify ExportClasses: SAM, EBAM, FindA0, sumSAM, sumEBAM 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: simulatorAPMS Exports: applyDeformationError, applyFNErrors, applyFPErrors, applyStickyError, compIndep, recordSticky, runAPComplex, runCompIndep, runSimulators, simulatorD, simulator, simulatorS Package: sizepower Exports: sampleSize.randomized, sampleSize.matched, power.randomized, power.matched, power.multi 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: snpMatrix Exports: epsout.ld.snp, filter.rules, glm.test.control, ibs.stats, ibsCount, ibsDist, impute.snps, imputation.maf, imputation.r2, imputation.nsnp, ld.snp, ld.with, misinherits, niceprint, pair.result.ld.snp, plot.snp.dprime, pool, print.snp.dprime, qq.chisq, read.HapMap.data, read.pedfile.info, read.pedfile.map, read.plink, read.snps.chiamo, read.snps.long, read.snps.pedfile, read.wtccc.signals, row.summary, col.summary, single.snp.tests, snp.cbind, snp.rbind, snp.compare, snp.clust.plot, 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.snp.matrix, xxt ExportMethods: cbind2, chi.squared, deg.freedom, effect.sign, is.na, ld.with, names, pool2, p.value, rbind2, show, summary, switch.alleles, plot, sample.size, effective.sample.size, [, [<-, coerce, initialize ExportClasses: snp.matrix, X.snp.matrix, snp, X.snp, snp.dprime, snp.reg.imputation, snp.tests.single, snp.tests.single.score, snp.tests.glm, snp.estimates.glm 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: splots Exports: plotScreen Package: spotSegmentation Exports: spotseg, spotgrid, plotBlockImage Package: sscore Exports: computeAffxSFandSDT, computeSFandSDT, SScore, SScoreBatch Package: ssize Exports: delta, delta.plot, pow, power.plot, power.t.test.FDR, ssize, ssize.plot 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: 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, readMappings, inverseList, whichAlgorithms, whichTests, GOplot, showSigOfNodes, getPvalues, showGroupDensity, reverseArch, nodesInInducedGraph, inducedGraph, buildLevels, getNoOfLevels, getGraphRoot, 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<-, score<-, testName<-, algorithm<-, printGenes, penalise, scoreOrder, testStatPar, printGraph, GenTable, GOFisherTest, GOKSTest, GOtTest, GOglobalTest, joinFun, allParents, expressionMatrix, phenotype ExportClasses: topGOdata, topGOresult, groupStats, classicCount, classicScore, classicExpr, weight01Count, weight01Score, weight01Expr, elimCount, elimScore, elimExpr, weightCount, pC, parentChild Package: tspair Exports: ts.pair, tspcalc, tspsig, tspplot Package: vbmp Exports: vbmp, predictCPP, predError, predLik, predClass, covParams, plotDiagnostics 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: 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, xcmsRaw, xcmsSet, xcmsFragments, xcmsPapply ExportMethods: absent, calibrate, collect, deepCopy, filepaths, filepaths<-, diffreport, fillPeaks, fillPeaks.MSW, fillPeaks.chrom, findPeaks.centWave, findPeaks.matchedFilter, findPeaks.MSW, findPeaks, getEIC, getPeaks, getScan, 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<-, searchMetlin, specDist, specDist.cosine, specDist.meanMZmatch, specDist.peakCount, show, simSearch, sortMz, write.cdf ExportClasses: xcmsEIC, xcmsPeaks, xcmsRaw, xcmsSet, xcmsFragments 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, bgcorrect, normalize, summarize, express, bgcorrect.mas4, bgcorrect.mas5, bgcorrect.rma, bgcorrect.gc, normalize.constant, normalize.quantiles, normalize.lowess, normalize.supsmu, summarize.mas4, summarize.mas5, summarize.rma, boxplot.dev, image.dev, mvaplot.dev, prefilter, unifilter, ProjectInfo, PreFilter, UniFilter, root.scheme, root.data, root.merge.data, root.expr, root.call, root.image, root.graph1D, root.graph2D, root.mvaplot, root.hist1D, root.hist2D, root.hist3D, root.density, root.profile, 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, attachCall, attachPVal, pvalData, pvalData<-, presCall, presCall<-, removeCall, removePVal, validCall, validPVal, callplot, attachExpr, exprs, exprs<-, exprType, exprType<-, mvaplot, normType, normType<-, nuseplot, rleplot, removeExpr, se.exprs, validExpr, validSE, xpsPreFilter, xpsUniFilter, addData, attachBgrd, attachInten, background, background<-, bgtreeNames, image, intensity, intensity<-, mm, pm, pmplot, rawCELName, removeBgrd, removeInten, validBgrd, xpsBgCorrect, xpsDABGCall, xpsFIRMA, xpsINICall, xpsMAS4, xpsMAS5, xpsMAS5Call, xpsNormalize, xpsPreprocess, xpsSummarize, xpsRMA, boxplot, getTreeData, hist, mboxplot, schemeFile, schemeFile<-, schemeSet, schemeSet<-, validData, attachMask, chipMask, chipMask<-, chipName, chipType, chipType<-, ncols, nrows, probeInfo, removeMask, export, fileDir, fileDir<-, initialize, root.browser, rootFile, rootFile<-, setName, setName<-, setType, setType<-, 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: 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