Package: ABarray
Exports: ABarray, ABarrayGUI, calcsn, concord, cvv, cvvPlot, doANOVA, doLPE, doPlotEset, doPlotFCT, doVennDiagram, drawVennDiagram, getMemberEset, getPantherMap, hclusterPlot, icpPlot, imputeFlag, lpe.fdr.BH, mamaplot, matrixPlot, mvaPair2, panel.cor, panel.scatter, qnNormalize, rgcolorsfunc, savejpg, scaleColorBar, snSummary

Package: ACME
Exports: do.aGFF.calc, findRegions, read.resultsGFF, findClosestGene, write.sgr, getRefflat
ExportMethods: show, print, plot, vals, threshold, cutpoints, chromosome, start, end
ExportClasses: aGFF, aGFFCalc, ACMESet, ACMECalcSet

Package: ADaCGH2
Exports: snowfallInit, pSegmentDNAcopy, pSegmentWavelets, pSegmentHMM, pSegmentBioHMM, pSegmentGLAD, pSegmentCGHseg, pSegmentHaarSeg, pChromPlot, inputDataToADaCGHData, outputToCGHregions

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
ExportMethods: show
ExportClasses: uRNAList

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: AnnotationFuncs
Exports: translate, pickRefSeq, pickRefSeq.Protein, pickRefSeq.mRNA, mapLists, removeNAs, pickGO, getEvidenceCodes, getOrthologs, .getTableName

Package: ArrayExpress
Exports: ArrayExpress, getAE, queryAE, magetab2bioc, getcolproc, getcolraw, procset, extract.zip

Package: ArrayExpressHTS
Exports: ArrayExpressHTS, ArrayExpressHTSFastQ, prepareReference, prepareAnnotation, initDefaultEnvironment, getPipelineOptions, getPipelineOption, setPipelineOptions, isRCloud

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: BHC
Exports: bhc, WriteOutClusterLabels

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, seqinfo, 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, summarize.peaks, read.bed, plot.overfitdiag, identify.overfitdiag, region.overfitdiag, plot.bed, plot.job, plot.PP

Package: BeadDataPackR
Exports: decompressBeadData, compressBeadData, readCompressedData, extractLocsFile

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: BioNet
Exports: saveNetwork, loadNetwork.sif, loadNetwork.tab, rmSelfLoops, makeNetwork, subNetwork, largestComp, largestScoreComp, permutateNodes, compareNetworks, getEdgeList, writeHeinzEdges, writeHeinzNodes, writeHeinz, runHeinz, scanFDR, readHeinzTree, readHeinzGraph, runFastHeinz, mapByVar, plot.bum, hist.bum, plotLLSurface, plotModule, plot3dModule, save3dModule, aggrPvals, fbum, fbumLL, bumOptim, print.bum, summary.bum, fitBumModel, fdrThreshold, piUpper, scoreOffset, scoreFunction, scoreNodes, getCompScores

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, 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, MIAxE, 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<-, get_xsbasetypes_conversion_lookup, alphabet, BString, DNAString, RNAString, AAString, BStringSet, DNAStringSet, RNAStringSet, AAStringSet, unsplit.list.of.XStringSet, XStringViews, unmasked, partitioning, BKeySortedData, DNAKeySortedData, RNAKeySortedData, AAKeySortedData, dataKey, dataTable, BKeySortedDataList, DNAKeySortedDataList, RNAKeySortedDataList, AAKeySortedDataList, xscat, BStringViews, adjacentViews, readFASTA, writeFASTA, read.BStringSet, read.DNAStringSet, read.RNAStringSet, read.AAStringSet, fasta.info, fastq.geometry, write.XStringSet, save.XStringSet, letter, letterFrequency, letterFrequencyInSlidingView, alphabetFrequency, hasOnlyBaseLetters, uniqueLetters, consensusMatrix, consensusString, mkAllStrings, oligonucleotideFrequency, dinucleotideFrequency, trinucleotideFrequency, nucleotideFrequencyAt, oligonucleotideTransitions, dinucleotideFrequencyTest, complement, reverseComplement, strrev, transcribe, cDNA, dna2rna, rna2dna, codons, translate, toComplex, replaceLetterAt, .inplaceReplaceLetterAt, injectHardMask, N50, FASTArecordsToCharacter, CharacterToFASTArecords, FASTArecordsToXStringViews, XStringSetToFASTArecords, read.XStringViews, write.XStringViews, subXString, 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, 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, DNAMultipleAlignment, RNAMultipleAlignment, AAMultipleAlignment, rowmask, rowmask<-, colmask, colmask<-, maskGaps, maskednrow, maskedncol, maskeddim, read.DNAMultipleAlignment, read.RNAMultipleAlignment, read.AAMultipleAlignment, consensusViews, write.phylip, detail, 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, nchar, names, names<-, [[, narrow, consensusMatrix, consensusString, alphabetFrequency, as.list, rowmask, rowmask<-, colmask, colmask<-, maskGaps, maskednrow, maskedncol, maskeddim, consensusViews, 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, letterFrequency, letterFrequencyInSlidingView, alphabetFrequency, hasOnlyBaseLetters, uniqueLetters, consensusMatrix, consensusString, oligonucleotideFrequency, nucleotideFrequencyAt, dinucleotideFrequencyTest, chartr, reverse, complement, reverseComplement, codons, translate, replaceLetterAt, maskMotif, injectHardMask, length, nchar, width, xsbasetype, xsbasetype<-, updateObject, 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, MultipleAlignment, DNAMultipleAlignment, RNAMultipleAlignment, AAMultipleAlignment, 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: CALIB
ExportMethods: show
ExportClasses: RGList_CALIB, SpikeList, ParameterList

Package: CAMERA
Exports: annotate, xsAnnotate, getpspectra, annotateDiffreport, getIsotopeCluster, findNeutralLossSpecs, findNeutralLoss
ExportMethods: calcCiS, calcCaS, calcIsotopes, calcPC, calcPC.lpc, calcPC.hcs, getAllPeakEICs, getPeaklist, plotPsSpectrum, plotEICs, show, findAdducts, groupCorr, findIsotopes, groupFWHM
ExportClasses: xsAnnotate

Package: CGEN
Exports: snp.scan.logistic, snp.logistic, recode.geno, getSummary, getWaldTest, QQ.plot, chromosome.plot, snp.effects, getMatchedSets, snp.matched, printEffects

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: CORREP
Exports: cor.balance, cor.bootci, cor.LRtest, cor.LRtest.std, cor.unbalance, permutest

Package: CRImage
Exports: calculateThreshold, segmentImage, createTrainingSet, createClassifier, classifyCells, calculateCellularity, processAperio

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: atomprop, pubchemFPencoding, read.SDFstr, read.SDFset, write.SDF, validSDF, makeUnique, atomcountMA, MW, MF, datablock2ma, splitNumChar, grepSDFset, conMA, bonds, groups, rings, plotStruc, SDF2apcmp, sdf2ap, apset2descdb, cmp.search, cmp.similarity, cmp.parse, cmp.parse1, sdf.subset, db.explain, cluster.sizestat, cmp.duplicated, sdf.visualize, db.subset, fp2bit, fpSim, getIds, searchString, searchSim, sdf2smiles, smiles2sdf, cmp.cluster, cluster.visualize
ExportMethods: sdfstr2list, sdf2list, sdf2str, SDFset2list, SDFset2SDF, sdfstr2list<-, SDFset2SDF<-, cid<-, header<-, atomblock<-, bondblock<-, datablock<-, [, [[, [<-, [[<-, coerce, show, length, c, plot, header, atomblock, bondblock, datablock, view, cid, sdfid, atomcount, datablocktag, ap
ExportClasses: SDFstr, SDF, SDFset, AP, APset

Package: ChromHeatMap
Exports: plotChrMap, makeChrStrandData, grabChrMapProbes, makeRangedDataList, createChrMatrix, chrHeatMap, drawMapDendro
ExportMethods: chrNames
ExportClasses: ChrStrandData, ChrStrandMatrix, ChrMapPlot

Package: Clonality
Exports: ave.adj.probes, chromosomePlots, clonality.analysis, genomewidePlots, histogramPlot, LOHclonality, splitChromosomes

Package: CoCiteStats
Exports: actorAdjTable, gene.geneslist.sig, gene.geneslist.statistic, gene.gene.statistic, paperLen, twowayTable, twTStats

Package: CoGAPS
Exports: CoGAPS, GAPS, calcCoGAPSStat, plotGAPS

Package: ConsensusClusterPlus
Exports: ConsensusClusterPlus, calcICL

Package: DEDS
Exports: aggregateFun, comp.adjp, comp.B, comp.ebayes, comp.F, comp.FC, comp.fdr, comp.modF, comp.modt, comp.SAM, comp.stat, comp.t, comp.unadjp, deds.calcAdjP, deds.calcFDR, deds.checkB, deds.checkclasslabel, deds.checkothers, deds.checkX, deds.chooseTest, deds.genExtra, deds.next.sample, deds.pval, deds.stat, deds.stat.linkC, euclidean, hist.DEDS, pairs.DEDS, qqnorm.DEDS, sam.fdr, sam.multiclass.func, sam.oneclass.func, sam.s0, sam.twoclass.func, test.checkX, topgenes, type2test

Package: DEGraph
Exports: AN.test, BS.test, getConnectedComponentList, getKEGGPathways, getSignedGraph, graph.T2.test, hyper.test, laplacianFromA, plotValuedGraph, randomWAMGraph, testOneConnectedComponent, testOneGraph, twoSampleFromGraph, writeAdjacencyMatrix2KGML

Package: DEGseq
Exports: DEGexp, DEGexp2, DEGseq, DEGseq.aln, DEGseq, getGeneExp, getGeneExp.aln, readGeneExp, samWrapper

Package: DESeq
Exports: newCountDataSet, counts, sizeFactors, sizeFactors<-, conditions, rawVarFunc, rawVarFuncTable, rawVarFuncTable<-, estimateSizeFactors, estimateVarianceFunctions, varianceFitDiagnosticsForMatrix, residualsEcdfPlotFromDiagnostics, varianceFitDiagnostics, residualsEcdfPlot, nbinomTest, getBaseMeansAndVariances, nbinomTest, estimateVarianceFunctionForMatrix, estimatePooledVarianceFunctionForMatrix, nbinomTestForMatrices, estimateSizeFactorsForMatrix, scvPlot, getVarianceStabilizedData, makeExampleCountDataSet, adjustScvForBias, varAdjFactors, varAdjFactors<-, nbinomGLMsForMatrix, nbinomFitGLM, nbkd.sf, nbinomGLMTest, getRawScvForSamplePair, getRawScvDistanceMatrix
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, getbdry, segment, segments.p, segments.summary, smooth.CNA, glFrequency, plotSample, zoomIntoRegion

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, as.raster.Image, Grayscale, TrueColor, Color, colorMode, colorMode<-, imageData, imageData<-, getFrame, 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, drawCircle, getFeatures, hullFeatures, edgeProfile, edgeFeatures, moments, cmoments, smoments, rmoments, haralickMatrix, haralickFeatures, zernikeMoments
ExportMethods: hist, show, Ops, [
ExportClasses: Image

Package: EBarrays
Exports: checkCCV, checkModel, checkVarsMar, checkVarsQQ, crit.fun, eb.createFamilyGG, eb.createFamilyLNN, eb.createFamilyLNNMV, ebPatterns, emfit, emfit0, emfit1, emfit2, emfit3, emfitmv, plot.ebarraysEMfit, plotCluster, plotMarginal, postprob

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

Package: ExiMiR
Exports: ReadExi, NormiR, make.gal.env, norm.miR, summarize.miR

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, smlSummary, MAFfilter, featureFilter, make_smlSet, GTFfilter
ExportMethods: chrnum, rsid, genesym, [, show, initialize, smList, smlEnv, probeId, exprs, [, plot_EvG, snpNames, phenoVar, plot, plot_EvG2, combine, getAlleles, snps, coerce, updateObject
ExportClasses: smlSet, gwSnpScreenResult, cwSnpScreenResult, chrnum, rsid, cnumOrMissing, genesym, probeId, phenoVar, snpdepth, SessionInfo, smlSummary, multiCisTestResult

Package: GGtools
Exports: eqtlTests, cisProxScores, clipPCs, pcChooser, permEx, topFeats, vcf2sm, externalize, getSS, manhPlot, makeDiagDirector, interleave2cis, exome_minp, topSnps, checkCommonSNPs, makeCommonSNPs, relocate
ExportMethods: gwSnpTests, topFeats, show
ExportClasses: eqtlTestsManager, multiCisDirector, cisProxScores

Package: GOSemSim
Exports: goSim, mgoSim, geneSim, mgeneSim, clusterSim, mclusterSim
ExportMethods: computeIC, loadGOMap, loadICdata, setCombineMethod<-, setMethod<-, setOntology<-, setOrganism<-, [, sim
ExportClasses: GOSet, GeneSet, GeneClusterSet, Params

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: rowt, rowF
ExportMethods: gsri, getGsri, getCdf, getParms, export, show, summary, plot, readCls, readGct, sortGsri
ExportClasses: Gsri

Package: GSVA
ExportMethods: gsva, filterGeneSets, computeGeneSetsOverlap

Package: GeneAnswers
Exports: categoryNet, chartPlots, drawTable, geneAnnotationHeatmap, geneAnswersBuilder, geneAnswersChartPlots, geneAnswersConceptNet, geneAnswersConcepts, geneAnswersHeatmap, geneAnswersHomoMapping, geneAnswersReadable, geneAnswersSort, geneConceptNet, getCategoryList, getCategoryTerms, getConceptTable, getDOLiteTerms, getGOList, getHomoGeneIDs, getPATHList, getPATHTerms, getSymbols, groupReport, searchEntrez, topCategory, topCategoryGenes, topDOLITE, topDOLITEGenes, topGO, topGOGenes, topPATH, topPATHGenes, topREACTOME.PATH, topREACTOME.PATHGenes, topcaBIO.PATH, topcaBIO.PATHGenes, geneAnswersConceptRelation, getConnectedGraph, getMultiLayerGraphIDs, getSingleLayerGraphIDs, getNextGOIDs, buildNet, getTotalGeneNumber, getREACTOMEPATHList, getREACTOMEPATHTerms, getcaBIOPATHList, getcaBIOPATHTerms, entrez2caBIO, caBIO2entrez, geneFunSummarize, plotGeneFunSummary, plotGraph, plotOntologyGraph, saveGeneFunSummary, simplifyGeneFunSummary
ExportMethods: getGeneInput, getTestType, getPValueT, getGenesInCategory, getGeneExprProfile, getAnnLib, getCategoryType, getEnrichmentInfo, setGeneInput, setTestType, setPValueT, setGeneExprProfile, setAnnLib, setCategoryType, setGenesInCategory, setEnrichmentInfo
ExportClasses: GeneAnswers

Package: GeneGA
Exports: GeneGA, GeneFoldGA, GeneCodon
ExportMethods: show, plotGeneGA
ExportClasses: GeneGA, GeneFoldGA

Package: GeneMeta
Exports: CountPlot, dstar, f.Q, IDRplot, multExpFDR, mu.tau2, sigmad, tau2.DL, var.tau2, zScoreFDR, zScorePermuted, zScores
ExportMethods: getdF

Package: 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: GeneSpring
Exports: BC2GSint, GSint, GSint2BC, GSload.exp, GSload.expBC, GSload.genelist, GSload.int, GSload.intBC, GSsave.exp, GSsave.genelist

Package: GeneTraffic
Exports: GTGetProjectList, GTGetProjectSummary, GTLoadExpression, GTLogin, GTLogout, GTServer
ExportClasses: GTServer

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, getSize, getGenomicRange
ExportClasses: DisplayPars, GenericArray, MappedRead, BaseTrack, Legend, Title, Gene, Transcript, GeneModel, GenomeAxis, ExonArray, GeneRegion, TranscriptRegion, Ideogram, gdObject, Overlay, RectangleOverlay, TextOverlay, AnnotationTrack, Segmentation, TrackOverlay, Smoothing, ImplementsTrackOverlay

Package: GenomicFeatures
Exports: loadFeatures, transcripts_deprecated, exons_deprecated, introns_deprecated, DEFAULT_CIRC_SEQS, makeTranscriptDb, supportedUCSCtables, supportedUCSCFeatureDbTracks, supportedUCSCFeatureDbTables, UCSCFeatureDbTableSchema, getChromInfoFromUCSC, makeTranscriptDbFromUCSC, getChromInfoFromBiomart, makeTranscriptDbFromBiomart, as.list, seqinfo, transcripts, exons, cds, transcriptsByOverlaps, exonsByOverlaps, cdsByOverlaps, id2name, transcriptsBy, exonsBy, cdsBy, intronsByTranscript, fiveUTRsByTranscript, threeUTRsByTranscript, transcriptWidths, transcriptLocs2refLocs, extractTranscripts, extractTranscriptsFromGenome, makeFeatureDbFromUCSC, features
ExportMethods: saveFeatures, metadata, show, as.list, seqinfo, transcripts, exons, cds, transcriptsByOverlaps, exonsByOverlaps, cdsByOverlaps, transcriptsBy, exonsBy, cdsBy, intronsByTranscript, fiveUTRsByTranscript, threeUTRsByTranscript
ExportClasses: GenomicFeatures, TranscriptDb

Package: GenomicRanges
Exports: validCigar, cigarOpTable, cigarToQWidth, cigarToWidth, cigarQNarrow, cigarNarrow, cigarToIRanges, cigarToIRangesListByAlignment, cigarToIRangesListByRName, queryLoc2refLoc, queryLocs2refLocs, splitCigar, cigarToRleList, cigarToCigarTable, summarizeCigarTable, seqinfo, seqinfo<-, seqnames, seqnames<-, seqlevels, seqlevels<-, seqlengths, seqlengths<-, isCircular, isCircular<-, isCircularWithKnownLength, Seqinfo, strand, strand<-, GRanges, GRangesList, rname, rname<-, cigar, qwidth, grglist, granges, grg, rglist, qnarrow, readGappedAlignments, GappedAlignments, SummarizedExperiment, assays, assays<-, assay, assay<-, rowData, rowData<-, colData, colData<-, exptData, exptData<-
ExportMethods: length, names, names<-, seqinfo, seqinfo<-, seqnames, seqnames<-, seqlevels, seqlevels<-, seqlengths, seqlengths<-, isCircular, isCircular<-, isCircularWithKnownLength, merge, coerce, as.data.frame, unlist, ranges, strand, elementMetadata, ranges<-, strand<-, elementMetadata<-, start, end, width, start<-, end<-, width<-, [, [<-, c, seqselect, seqselect<-, split, window, flank, resize, shift, disjoin, gaps, range, reduce, coverage, duplicated, unique, order, sort, rank, ==, <=, >=, <, >, union, intersect, setdiff, punion, pintersect, psetdiff, findOverlaps, countOverlaps, match, %in%, show, rname, rname<-, cigar, qwidth, grglist, granges, grg, rglist, ngap, qnarrow, dimnames, dimnames<-, precede, follow, countGenomicOverlaps
ExportClasses: Seqinfo, GenomicRanges, GRanges, GRangesList, GappedAlignments, SummarizedExperiment

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: GraphAT
Exports: clust2Mat, getpvalue, makeClustM, mat2UndirG, permEdgesM2M, permNodesM2M, permPower

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: HEM
Exports: am.tran, am.tran.half, base.ASE.Olig, base.error.Olig, base.error.Olig.quanOnly, base.PSE.Olig, boot.base.ASE.Olig, boot.base.error.Olig, boot.base.PSE.Olig, fixbound.predict.smooth.spline, hem, hem.eb.prior, hem.fdr, hem.null.no, hem.null.one, hem.null.two, hem.preproc, nonpar.error.Olig, nonpar.no.error.Olig, nonpar.rep.error.Olig, par.error.Olig, par.no.error.Olig, par.rep.error.Olig, permut, quant.normal, quant.normal2, remove.sig.genes

Package: HTSanalyzeR
Exports: aggregatePvals, annotationConvertor, biogridDataDownload, celAnnotationConvertor, cellHTS2OutputStatTests, collectionGsea, drosoAnnotationConvertor, duplicateRemover, FDRcollectionGsea, analyzeGeneSetCollections, GOGeneSets, gseaPlots, gseaScores, gseaScoresBatch, gseaScoresBatchParallel, HTSanalyzeR4cellHTS2, KeggGeneSets, mammalAnnotationConvertor, multiHyperGeoTest, networkAnalysis, networkPlot, pairwiseGsea, pairwiseGseaPlot, pairwisePhenoMannWhit, permutationPvalueCollectionGsea, hyperGeoTest, writeReportHTSA
ExportMethods: analyze, reportAll, plotSubNet, viewSubNet, viewEnrichMap, plotEnrichMap, plotGSEA, viewGSEA, writeHits, getTopGeneSets, appendGSTerms, interactome, preprocess, show, summarize, report
ExportClasses: GSCA, NWA

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, plotCtArray, plotCtBoxes, plotCtCategory, plotCtCor, plotCtDensity, plotCtHeatmap, plotCtHistogram, plotCtOverview, plotCtPCA, plotCtReps, plotCtRQ, plotCtScatter, plotCtSignificance, plotCtVariation, plotCVBoxes, plotCtLines, plotCtCard, rbind.qPCRset, readCtData, setCategory, setCt<-, summary, ttestCtData, plotCtPairs
ExportMethods: [, exprs, exprs<-, featureNames, featureNames<-, sampleNames, sampleNames<-, show, summary
ExportClasses: qPCRset

Package: Harshlight
Exports: HarshComp, HarshExt, Harshlight

Package: Heatplus
Exports: cutplot.dendrogram, heatmap_2, heatmap_plus, picketplot, RainbowPastel, RGBColVec

Package: HilbertVis
Exports: hilbertCurve, hilbertCurvePoint, plotHilbertCurve, shrinkVector, plotLongVector, makeWiggleVector, hilbertImage, makeRandomTestData, showHilbertImage

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

Package: IPPD
ExportMethods: show, getPeaklist, fitModelParameters, threshold, visualize
ExportClasses: peaklist, modelfit

Package: IRanges
Exports: setValidity2, new2, isTRUEorFALSE, isSingleInteger, isSingleNumber, isSingleString, isSingleNumberOrNA, isSingleStringOrNA, normargShift, normargWeight, fold, isConstant, safeExplode, strsplitAsListOfIntegerVectors, svn.time, solveUserSEW0, IRanges, solveUserSEW, successiveIRanges, breakInChunks, 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, endoapply, mendoapply, seqapply, mseqapply, tseqapply, seqsplit, seqby, 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, distance, 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, compact, 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<-, evalSeparately, subsetByFilter, reducerFun, reducerFun<-, reducerParams, reducerParams<-, iteratorFun, iteratorFun<-, 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, which.max, which.min, 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, ifelse, c, union, intersect, setdiff, merge, split, splitRanges, eval, with, within, t, is.na, na.omit, na.exclude, complete.cases, %in%, by, match, Reduce, Filter, Find, Position, updateObject, isConstant, 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, compact, 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, DataTable, DataTableORNULL, Vector, List, 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: IsoGeneGUI
Exports: IsoGeneGUI, IsoGeneGUIHelp

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, get.ko.by.gene, get.ko.by.ko.class, get.genes.by.ko.class, get.genes.by.ko, get.kos.by.pathway, get.pathways.by.kos

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: LVSmiRNA
Exports: RLM, estVC, estVC.EList, estVC.RGList, lvs, lvs.EList, lvs.RGList, normalize.lvs, plot, read.mir, summarize, summarize.EList, rlmFit, summarize.RGList
ExportMethods: plot, exprs, exprs<-, preproc, preproc<-, boxplot, sampleNames, featureNames, probeNames

Package: LiquidAssociation
ExportMethods: CNM.full, CNM.simple, getsGLA, getsLA, GLA, LA, plotGLA

Package: MBCB
Exports: mbcb.parseFile, mbcb.correct, mbcb.main, bg.rma, bg.mcmc, mbcb.gui

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: MEDIPS
ExportMethods: bin_size, calcurve_mean_coupling, calcurve_mean_signals, calcurve_var, cali_chr, chr_lengths, chr_names, distFile, distFunction, extend, fragmentLength, genome_CF, genome_chr, genome_name, genome_norm, genome_pos, genome_raw, intercept, number_pattern, number_regions, pattern_chr, pattern_pos, regions_chr, regions_start, regions_stop, regions_strand, sample_name, seq_pattern, show, slope
ExportClasses: MEDIPSset

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: MLP
Exports: getGeneSets, mlpBarplot, MLP, plotGeneSetSignificance, plotGOgraph, plot.MLP

Package: MSnbase
Exports: readMzXMLData, formatRt, extractSpectra, extractPrecSpectra
ExportMethods: show, [, [[, fileNames, qual, length, plot, plot2d, spectra, processingData, peaksCount, clean, removePeaks, intensity, mz, tic, fromFile, precursorMz, precursorIntensity, precursorCharge, acquisitionNum, rtime, peaksCount, msLevel, collisionEnergy, polarity, trimMz, quantify, header, dim, multiplex, multiLabels, width, reporterNames, reporterNames<-, reporterColours, reporterColors
ExportClasses: pSet, MIAPE, MSnExp, MSnProcess, MSnSet, Spectrum, Spectrum1, Spectrum2, ReporterIons

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: MantelCorr
Exports: ClusterGeneList, ClusterList, DistMatrices, GetClusters, MantelCorrs, PermutationTest

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: MiPP
Exports: cv.mipp.rule, get.mipp, get.mipp.lda, get.mipp.logistic, get.mipp.qda, get.mipp.svm.linear, get.mipp.svm.rbf, linearkernel.decision.function, mipp, mipp.preproc, mipp.rule, mipp.seq, pre.select, quant.normal, quant.normal2, rbfkernel.decision.function

Package: MotIV
Exports: motifMatch, generateDBScores, readDBScores, writeDBScores, getGademPWM, readGademPWMFile, readPWMfile, viewAlignments, summary, plot, split, filter, makePWM, setFilter, combineMotifs, trimPWMedge, exportAsRangedData, similarity, viewMotifs, occurences, cooccurences, getPWM, nMotifs, motifDistances, motifHclust, motifCutree
ExportMethods: show, summary, combineMotifs, filter, split, exportAsTransfacFile, getPWM
ExportClasses: motiv, matches, alignments, transcriptionFactor, filter

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

Package: NCIgraph
Exports: getNCIPathways, getSubtype.NCIgraph, is.NCIgraph, parseNCInetwork, translateNCI2GeneID
ExportClasses: NCIgraph

Package: NTW
Exports: P.preestimation, NTW, AP.estimation.Srow, A.estimation.Srow, backward, forward, method.geo, method.sse, method.ml, comb.matrix

Package: NuPoP
Exports: predNuPoP, readNuPoP, plotNuPoP

Package: OCplus
Exports: approx2d, average.fdr, brk2mid, CDF, CDF.paired, CDFmix, CDFmix.paired, df2var, dgfree, dmt, dmt.paired, dmtmix, dmtmix.paired, DoConstrain, DrawContourlines, EOC, FDR, FDR.paired, fdr1d, fdr2d, FDRp, gausei, lfdr, lfdr.paired, MAsim, MAsim.real, MAsim.smyth, MAsim.var, MidBreaks, MidBreaks.t, OCshow, p0, PermNull, plot.FDR.result, plot.fdr1d.result, plot.fdr2d.result, Rinv, rmatrix, samplesize, smooth1d, smooth2d.basic, smooth2d.direct, summary.fdr.result, tMixture, TOC, topDE, Tornadoplot, tstatistics, Volcanoplot

Package: 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: OrderedList
Exports: check.test.args, compareLists, getOverlap, OrderedList, overlap, plot.listComparison, plot.listComparisonOverlap, plot.OrderedList, plot.shuffledRandomScores, prepareData, preparePermutations, print.listComparison, print.listComparisonOverlap, print.OrderedList, print.shuffledRandomScores, scoreOrderComparison, scoreOrderComparisonBoth, scoreRankings, shuffledRandomScores, test.fc, test.t, test.z

Package: 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: PatientGeneSets
Exports: do.gene.set.analysis, sim.data.p.values, cma.scores, extract.sims.method, combine.sims
ExportMethods: show
ExportClasses: SetMethodsSims

Package: R453Plus1Toolbox
Exports: extendedCIGARToList, listToExtendedCIGAR
ExportMethods: alignShortReads, readsOnTarget, coverageOnTarget, calculateTiTv, genomeSequencerMIDs, sequenceCaptureLinkers, demultiplexReads, removeLinker, filterChimericReads, detectBreakpoints, mergeBreakpoints, annotateVariants, annotatedVariants, htmlReport, plotVariationFrequency, plotAmpliconCoverage, plotVariants, plotChimericReads, seqsC1, seqsC1<-, seqsC2, seqsC2<-, commonBpsC1, commonBpsC1<-, commonBpsC2, commonBpsC2<-, commonAlignC1, commonAlignC1<-, commonAlignC2, commonAlignC2<-, alignedReadsC1, alignedReadsC1<-, alignedReadsC2, alignedReadsC2<-, MapperSet, AVASet, fDataAmp, featureDataAmp, featureDataAmp<-, assayDataAmp, assayDataAmp<-, getAlignedReads, referenceSequences, referenceSequences<-, getReadStatus, getVariantPercentages, setVariantFilter
ExportClasses: AVASet, MapperSet, AnnotatedVariants, Breakpoints

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: RCytoscape
Exports: CytoscapeConnection, new.CytoscapeWindow, CytoscapeWindow, existing.CytoscapeWindow, noa.names, noa, eda.names, eda, cy2.edge.names, makeSimpleGraph, makeRandomGraph, initNodeAttribute, initEdgeAttribute, validCyWin
ExportMethods: deleteWindow, deleteAllWindows, displayGraph, getArrowShapes, getLayoutNames, getLayoutNameMapping, getLayoutPropertyNames, getLayoutPropertyType, getLayoutPropertyValue, setLayoutProperties, getLineStyles, getNodeShapes, getDirectlyModifiableVisualProperties, getAttributeClassNames, getWindowCount, getWindowID, getWindowList, layout, setPosition, getPosition, ping, redraw, raiseWindow, setWindowSize, getZoom, setZoom, setCenter, getCenter, showGraphicsDetails, fitContent, fitSelectedContent, getViewCoordinates, sendNodes, sendEdges, setNodeAttributes, setNodeAttributesDirect, setEdgeAttributes, setEdgeAttributesDirect, addCyNode, addCyEdge, addGraphToGraph, dockPanel, floatPanel, hidePanel, hideAllPanels, setDefaultNodeShape, setDefaultNodeColor, setDefaultNodeSize, setDefaultNodeColor, setDefaultNodeBorderColor, setDefaultNodeBorderWidth, setDefaultNodeFontSize, setDefaultNodeLabelColor, setDefaultEdgeLineWidth, setDefaultEdgeColor, setNodeTooltipRule, setEdgeTooltipRule, setNodeLabelRule, setEdgeLabelRule, setNodeColorRule, setNodeBorderColorRule, setNodeBorderWidthRule, setNodeShapeRule, setNodeSizeRule, setEdgeLineStyleRule, setEdgeLineWidthRule, setEdgeTargetArrowRule, setEdgeSourceArrowRule, setEdgeTargetArrowColorRule, setEdgeSourceArrowColorRule, setEdgeColorRule, setEdgeOpacityDirect, setNodeSizeDirect, setNodeWidthDirect, setNodeHeightDirect, setNodeLabelDirect, setNodeFontSizeDirect, setNodeShapeDirect, setNodeImageDirect, setNodeColorDirect, setNodeOpacityDirect, setNodeFillOpacityDirect, setNodeBorderOpacityDirect, setNodeLabelOpacityDirect, setEdgeColorDirect, setEdgeLabelDirect, setEdgeFontSizeDirect, setEdgeLabelColorDirect, setEdgeTooltipDirect, setEdgeLineWidthDirect, setEdgeLineStyleDirect, setEdgeSourceArrowShapeDirect, setEdgeTargetArrowShapeDirect, setEdgeSourceArrowColorDirect, setEdgeTargetArrowColorDirect, setEdgeLabelOpacityDirect, setEdgeSourceArrowOpacityDirect, setEdgeTargetArrowOpacityDirect, setEdgeLabelWidthDirect, getNodeCount, getEdgeCount, getNodeAttribute, getAllNodeAttributes, getEdgeAttribute, getAllEdgeAttributes, getNodeAttributeNames, getEdgeAttributeNames, deleteNodeAttribute, deleteEdgeAttribute, getAllNodes, getAllEdges, clearSelection, selectNodes, invertNodeSelection, deleteSelectedNodes, getSelectedNodes, getSelectedNodeCount, selectEdges, getSelectedEdges, getSelectedEdgeCount, hideSelectedEdges, invertEdgeSelection, deleteSelectedEdges, createWindowFromSelection, getFirstNeighbors, selectFirstNeighborsOfSelectedNodes, getGraph, setGraph, hideNodes, unhideNodes, hideSelectedNodes, unhideAll, version, msg, clearMsg, getGraphFromCyWindow, getVisualStyleNames, copyVisualStyle, setVisualStyle, lockNodeDimensions, getDefaultBackgroundColor, setDefaultBackgroundColor, getDefaultNodeSelectionColor, setDefaultNodeSelectionColor, getDefaultNodeReverseSelectionColor, setDefaultNodeReverseSelectionColor, getDefaultEdgeSelectionColor, setDefaultEdgeSelectionColor, getDefaultEdgeReverseSelectionColor, setDefaultEdgeReverseSelectionColor, saveImage, saveNetwork
ExportClasses: CytoscapeWindowClass, CytoscapeConnectionClass

Package: RDRToolbox
Exports: Isomap, LLE, generateData, plotDR, SwissRoll, DBIndex

Package: RLMM
Exports: Classify, create_Thetafile, normalize_Rawfiles, plot_theta

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

Package: RNAinteract
Exports: createCellHTSFromFiles, createRNAinteract, createRNAinteractFromFiles, getData, getMain, getMainNeg, getReplicateData, getIndDesignData, getChannelNames, getScreenNames, getScale, sgisubset, bindscreens, summarizeScreens, estimateMainEffect, normalizeMainEffectQuery, normalizeMainEffectTemplate, normalizePlateEffect, computePI, computePValues, embedPCA, plotDoublePerturbation, doublePerturbationGrob, grid.doublePerturbation, postDrawDetails.doublePerturbation, plotHeatmap, grid.sgiHeatmap, startReport, endReport, reportAnnotation, reportDoublePerturbation, reportGeneLists, reportHeatmap, reportMainEffects, reportNetworks, reportScreenData, reportStatistics
ExportClasses: RNAinteract

Package: RNAither
Exports: createSubset, indexSubset, findReplicates, orderGeneIDs, rms, trim, closestToZero, furthestFromZero, divideChannels, eraseDataSetColumn, generateReplicateMat, generateRepMatNoFilter, summarizeReps, summarizeRepsNoFiltering, sumChannels, generateDatasetFile, joinDatasets, joinDatasetFiles, gseaAnalysis, LiWongRank, varAdjust, divNorm, quantileNormalization, BScore, ZScore, ZScorePerScreen, subtractBackground, lowessNorm, controlNorm, saveDataset, saveOldIntensityColumns, discardLabtek, discardWells, channelPlot, plotBar, ZScorePlotTwo, numCellQualControl, percCellQualControl, ZPRIMEQualControl, SNRQualControl, DRQualControl, plotControlHisto, plotControlHistoPerplate, plotControlHistoPerscreen, plotHisto, plotHistoPerplate, plotHistoPerscreen, plotQQ, plotQQperplate, plotQQperscreen, replicatesSpearmancor, replicatesCV, makeBoxplotControls, makeBoxplotControlsPerPlate, makeBoxplotControlsPerScreen, makeBoxplotPerScreen, makeBoxplotPerPlate, makeBoxplot4PlateType, spatialDistrib, compareReplicates, compareReplicaPlates, compareReplicateSD, compareReplicateSDPerScreen, controlDensity, controlDensityPerScreen, controlDensityPerPlate, ZScorePlot, Ttest, MannWhitney, RankProduct, multTestAdjust, savepValVec, incorporatepValVec, hitselectionPval, hitselectionZscore, hitselectionZscorePval, spatialDistribHits, volcanoPlot, vennDiag, compareHits, mainAnalysis, rnaither

Package: ROC
Exports: AUC, AUCi, dxrule.sca, pAUC, pAUCi, ROC, rocdemo.sca, trapezint
ExportMethods: plot, points, lines
ExportClasses: rocc

Package: RPA
Exports: estimate.affinities, get.probe.noise.estimates, rpa, rpa.fit, RPA.dcost, rpa2eset, RPA.iteration, rpa.plot, plot.rpa, RPA.pointestimate, RPA.preprocess, set.priors
ExportMethods: [, [[, show
ExportClasses: rpa, rpa.fit, 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: RankProd
Exports: NaReplace, NaReplace2, Newdata, NewdataCom, OriginxyCall, OriginxyCall2, plotGene, plotRP, RankComp, RankProd1, RankProd2, RankSum, RP, RPadvance, RSadvance, topGene, xyCall

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, BamFile

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: SLqPCR
Exports: geneStabM, geomMean, normPCR, relQuantPCR, selectHKgenes

Package: SMAP
Exports: SMAPHMM, SMAPObservations
ExportMethods: name, value, noObservations, chromosome, startPosition, endPosition, reporterId, A, Pi, Phi, noStates, HMM, observations, P, Q, smap, initialize, show, plot
ExportClasses: SMAPObservations, SMAPHMM, SMAPProfile, SMAPProfiles

Package: 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, combfunc

Package: SQUADD
Exports: simResService
ExportMethods: [, [<-, getFittedTable, plotCC, plotPredMap, plotSimMatrix
ExportClasses: SquadSimResServiceImpl

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%, c

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, writeWIG

Package: TDARACNE
Exports: TDARACNEdataPublished, TDARACNE

Package: TEQC
Exports: chrom.barplot, coverage.correlation, coverage.density, coverage.hist, coverage.GC, coverage.plot, coverage.target, coverage.targetlength.plot, coverage.uniformity, covered.k, duplicates.barplot, fraction.reads.target, fraction.target, get.baits, get.reads, get.targets, insert.size.hist, make.wigfiles, reads2pairs, readsPerTarget

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: TurboNorm
Exports: pspline, normalize.pspline, normalize.AffyBatch.pspline, turbotrend, panel.pspline

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: Vega
Exports: vega, plotSegmentation

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: a4Base
Exports: probe2gene, a4palette, filterVarInt, tTest, limmaTwoLevels, propDEgenes, histPvalue, histpvalueplotter, propdegenescalculation, volcanoPlot, volcanoplotter, lassoReg, logReg, probabilitiesPlot, plot1gene, plotCombination2genes, boxPlot, plotComb2Samples, plotCombMultSamples, profilesPlot, addQuantilesColors, combineTwoExpressionSet, computeLogRatio, plotLogRatio, createExpressionSet, replicates, heatmap.expressionSet
ExportMethods: propDEgenes, histPvalue, volcanoPlot, topTable, spectralMap
ExportClasses: ExpressionSetWithComputation

Package: a4Classif
Exports: lassoClass, pamClass, rfClass, ROCcurve

Package: a4Core
Exports: confusionMatrix, simulateData
ExportMethods: topTable

Package: a4Preproc
Exports: addGeneInfo

Package: a4Reporting
Exports: annotationTable, generateEntrezIdLinks, generateGOIdLinks, print.xtableAnnotationTable
ExportMethods: xtable
ExportClasses: annotationTable

Package: 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: affyQCReport
Exports: affyQAReport, borderQC1, borderQC2, correlationPlot, openQAReport, QCReport, rmQAReport, signalDist, titlePage

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

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, blastSequences
ExportMethods: abstText, articleTitle, authors, chromInfo, chromLengths, chromLocs, chromNames, dataSource, Definition, fileName, geneSymbols, GOID, homoACC, homoHGID, homoLL, homoOrg, homoPS, homoType, homoURL, initialize, journal, mainPage, nChrom, Ontology, organism, pageText, pageTitle, pmid, probesToChrom, pubDate, pubMedAbst, Secondary, show, sidePage, Synonym, Term, toFile, topPage
ExportClasses: chromLocation, FramedHTMLPage, homoData, HTMLPage, pubMedAbst

Package: annotationTools
Exports: compactList, getANNOTATION, getGENEID, getGENEONTOLOGY, getGENESYMBOL, getGENETITLE, getHOMOLOG, getMULTIANNOTATION, getOrthologousProbesets, getPROBESET, listToCharacterVector, ps2ps

Package: anota
Exports: anotaPerformQc, anotaResidOutlierTest, anotaGetSigGenes, anotaPlotSigGenes

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, prepdata, prepaffy, aqm.writereport, aqm.boxplot, aqm.maplot, aqm.density, aqm.probesmap, aqm.meansd, aqm.heatmap, aqm.pca, aqm.rle, aqm.nuse, aqm.rnadeg, aqm.pmmm, aqm.spatial, addXYfromGAL, outliers, boxplotOutliers
ExportClasses: aqmReportModule, outlierDetection

Package: attract
ExportClasses: SynExpressionSet, AttractorModuleSet

Package: baySeq
ExportMethods: dim, [, show
ExportClasses: countData

Package: beadarray
Exports: insertBeadData, removeBeadData, getBeadData, plotChipLayout, createTargetsFile, quickSummary, getAnnotation, setAnnotation, summarize, illuminaOutlierMethod, beadStatusVector, insertSectionData, backgroundCorrectSingleSection, beadarrayUsersGuide, checkPlatform, readIllumina, readLocsFile, convertBeadLevelList, processSwathData, readTIFF, plotTIFF, illuminaForeground, illuminaBackground, illuminaSharpen, medianBackground, logGreenChannelTransform, logRedChannelTransform, logRatioTransform, greenChannelTransform, redChannelTransform, plotBeadIntensities, genericBeadIntensityPlot, poscontPlot, outlierplot, imageplot, checkRegistration, makeQCTable, expressionQCPipeline, calculateOutlierStats, controlProbeDetection, plotBeadLocations, BASH, HULK, generateNeighbours, BASHCompact, BASHDiffuse, BASHExtended, setWeights, showArrayMask, readBeadSummaryData, plotMAXY, normaliseIllumina, medianNormalise, calculateDetection
ExportMethods: show, [[, dim, sectionNames, numBeads, boxplot, exprs, se.exprs, nObservations, Detection, se.exprs<-, exprs<-, nObservations<-, Detection<-, qcData, combine
ExportClasses: BeadLevelList, beadLevelData, ExpressionSetIllumina, illuminaChannel

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: biocGraph
Exports: imageMap

Package: biocViews
Exports: writeBiocViews, getBiocViews, write_VIEWS, write_REPOSITORY, genReposControlFiles, extractVignettes, extractManuals, writeRepositoryHtml, writePackageDetailHtml, getSubTerms, getBiocSubViews, writeTopLevelView, writeHtmlDoc, write_SYMBOLS, writeRFilesFromVignettes
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, buildCellHTS2, channelNames<-, 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<-, channelNames<-, 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, dmrPlot, regionPlot, 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: chopsticks
Exports: epsout.ld.snp, filter.rules, Fst, 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, plotUncertainty, pool, print.snp.dprime, qq.chisq, read.HapMap.data, read.pedfile.info, read.pedfile.map, read.beagle, read.impute, read.mach, 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.plink, write.snp.matrix, wtccc.sample.list, 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: clippda
Exports: sampleClusteredData, negativeIntensitiesCorrection
ExportMethods: show
ExportClasses: aclinicalProteomicsData

Package: clst
Exports: partition, findThreshold, plotDistances, plotMutinfo, classifier, classify, classifyIter, printClst, pull, pullTab, scaleDistPlot

Package: clstutils
Exports: classifyPlacements, treeDists, maxDists, findOutliers, refpkgContents, taxonomyFromRefpkg, prettyTree

Package: clusterProfiler
Exports: compareCluster, enrichGO, enrichKEGG, groupGO
ExportMethods: plot, summary, show
ExportClasses: groupGOResult, enrichKEGGResult, enrichGOResult, compareClusterResult

Package: clusterStab
ExportMethods: ecdf, hist, benhur, clusterComp
ExportClasses: BenHur, ClusterComp

Package: cn.farms
Exports: combineData, createAnnotation, createMatrix, distributionDistance, dnaCopySf, fragLengCorr, mlSummarization, normalizeAverage, normalizeCels, normalizeNpData, plotDendrogram, plotDensity, plotEvalIc, plotRegions, plotSmoothScatter, plotViolines, slSummarization, sparseFarmsC, summarizeFarmsExact, summarizeFarmsGaussian, summarizeFarmsMethods, summarizeFarmsStatistics, summarizeFarmsVariational, summarizeWindowBps, summarizeWindowMethods, summarizeWindowStd

Package: coRNAi
Exports: cellHTS2df, df2lmFit, SDplot, MAplot, rlmmain, WithinScreenPlot, BetweenScreenPlot, updateDf, InteractLevelPlot, BoxPlotShorth, MainFitPlot, df2array, lmmain, estmodel, weightDf, PlotHeatmap, df2fitmatrix, interactiontable, tt2matrix, cortestmatrices, data2graph, Pplot

Package: 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, crlmmIllumina, crlmmIlluminaV2, genotype, readIdatFiles, snprma, snprma2, crlmm2, genotype2, genotypeLD, genotype.Illumina, crlmmCopynumber2, crlmmCopynumberLD, crlmmCopynumber, totalCopynumber, rawCopynumber, constructInf, preprocessInf, genotypeInf
ExportMethods: A, B, nuA, nuB, phiA, phiB, corr, tau2, Ns, medians, mads, CA, CB, lines

Package: ctc
Exports: hc2Newick, hclust2treeview, r2cdt, r2atr, r2gtr, r2cluster, r2xcluster, read.eisen, xcluster, xcluster2r

Package: cycle
Exports: ar1analysis, backgroundData, fdrfourier, fourierscore

Package: daMA
Exports: analyseMA, cinfo, cinfoB.AB, cmat, cmatB.AB, core, designMA, designs.basic, designs.composite

Package: ddCt
Exports: barploterrbar, ddCtAbsolute, elist, errBarchart, SDMFrame, CSVFrame, readSDM, ColMap, replaceVectorByEquality, write.htmltable, writeSimpleTabCsv, getDir
ExportMethods: coreData, coreData<-, rightCensoring, fileNames, sampleNames, sampleNames<-, uniqueDetectorNames, uniqueDetectorNames<-, uniqueSampleNames, uniqueSampleNames<-, detectorNames<-, detectorNames, replaceDetector, replaceSample, removeDetector, removeSample, removeNTC, level, levelErr, Ct, Ct<-, CtErr, dCt, dCtErr, ddCt, ddCtErr, numberCt, numberNA, ddCtExpression, errBarchart, InputFrame, elistWrite
ExportClasses: ddCtExpression, InputFrame, InputReader, SDMReader, CSVReader, ColMap

Package: diffGeneAnalysis
Exports: assocAnalysis, biasAdjust, curveFit, dataTrim, normalize, refGroup

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, DGEExact, TopTags, DGEGLM, DGELRT

Package: eisa
Exports: ISA, ISANormalize, ISAIterate, ISAUnique, ISASweep, ISASweepGraph, ISASweepGraphPlot, ISARobustness, ISAFilterRobust, ISAEnrichment, ISAGO, ISAKEGG, ISACHR, ISAmiRNA, gograph, gographPlot, expPlotCreate, expPlotColbar, expPlot, condPlot, overlap, overlapPlot, mnplot, ISAmnplot, ISA2heatmap, profilePlot, ISAHTMLTable, ISAHTMLModules, ISAHTML, annotate
ExportMethods: coerce, summary, htmlReport, pvalues, geneCounts, oddsRatios, expectedCounts, universeCounts, universeMappedCount, geneMappedCount, geneIdUniverse, 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: 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: fabia
Exports: fabia, fabias, fabiap, mfsc, fabiasp, fabi, projFunc, projFuncPos, estimateMode, nmfsc, nmfeu, nmfdiv, matrixImagePlot, plotBicluster, extractPlot, extractBic, makeFabiaData, makeFabiaDataBlocks, makeFabiaDataPos, makeFabiaDataBlocksPos, fabiaDemo, fabiaVersion
ExportMethods: plot, summary, show, showSelected
ExportClasses: Factorization

Package: factDesign
Exports: contrastTest, findFC, kRepsOverA, madOutPair, outlierPair, par2lambda

Package: farms
Exports: expFarms, qFarms, lFarms, generateExprVal.method.farms
ExportMethods: summary, plot, INIcalls, getI_Eset, getNI_Eset, getI_ProbeSets, getNI_ProbeSets
ExportClasses: INI_Calls

Package: fdrame
Exports: compute.f.statistic, compute.resampling.stat, compute.statistic, compute.t.statistic, fdr.adaptive.c, fdr.adaptive.c.resampling, fdr.basic.comp, fdr.bh, fdr.error, fdr.gui, fdr.ma, fdr.plot, fdr.pt, fdr.q, fdr.qu, gene.expression.normalization, get.resampling.statistic.array, OnBrowseDesign, OnBrowseInput, OnBrowseOutput, OnCancel, OnCbfa1, OnCbfa2, OnCbfa3, OnCbfa4, OnCompute, OnHelp, OnOK, OnRbfa1, OnRbfa2, OnRbfa3, OnRbfa4, OnRbpm1, OnRbpm2, read.matrix

Package: 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%, estimateLogicle
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: flowPlots
Exports: GroupListBoxplot, makeDataList, makeBarplotData, makeTernaryData, legendPFDStatsGroupNames, computePFDGroupStatsList
ExportMethods: stackedData, pfdData, pfdPartsData, marginalData, markers, profileData, stackedData<-, pfdData<-, pfdPartsData<-, marginalData<-, markers<-, profileData<-, computeMarkers, readStackedData, computeProfileData, computeMarginalData, computePFDData, computePFDPartsData
ExportClasses: StackedData

Package: flowQ
Exports: validProcess, qaProcess, aggregatorList, qaGraph, qaGraphList, qaProcessFrame, writeQAReport, qaReport, qaProcess.marginevents, qaProcess.timeline, qaProcess.timeflow, qaProcess.cellnumber, qaProcess.2DStatsPlot, qaProcess.ECDFPlot, qaProcess.DensityPlot, qaProcess.KLDistPlot, qaProcess.BoundaryPlot, locateDuplicatedParameters, normalizeSets, writeQATextReport, txtFormatQAObject, preProcessFlowList, binaryAggregator, discreteAggregator, factorAggregator, stringAggregator, numericAggregator, rangeAggregator, evaluateProcess
ExportMethods: outliers, initialize, show, names, writeLines
ExportClasses: outlierResult, qaAggregator, binaryAggregator, discreteAggregator, factorAggregator, stringAggregator, numericAggregator, rangeAggregator, aggregatorList, qaGraph, qaGraphList, qaProcessFrame, qaProcess, qaProcessSummary

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

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, GNUSE
ExportMethods: initialize, se.exprs, weights, residuals, randomeffects, as.ExpressionSet
ExportClasses: frmaExpressionSet

Package: frmaTools
Exports: makeVectorsAffyBatch, makeVectorsExonFeatureSet, makeVectorPackage, convertPlatform

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: gage
Exports: eg2sym, sym2eg, essGene, esset.grp, gage, gagePrep, gageSum, gageComp, gagePipe, geneData, gs.tTest, gs.zTest, gs.KSTest, heter.gage, pairData, readExpData, readList, sigGeneSet

Package: gaggle
Exports: gaggleInit, getNameList, getCluster, getMatrix, getNetwork, getTuple, broadcast, geese, getTargetGoose, setTargetGoose, setSpecies, getSpecies, showGoose, hideGoose, testGagglePackage, connectToGaggle, disconnectFromGaggle, getJavaClassName, getTupleAsList, tupleToList, newSingle, addSingle, newTuple

Package: gaia
Exports: runGAIA, load_cnv, load_markers

Package: gcrma
Exports: average.for.PAV, base.profiles, base.profiles.mm, base.profiles.nc, bg.adjust.affinities, bg.adjust.constant, bg.adjust.fullmodel, bg.adjust.gcrma, bg.adjust.mm, bg.adjust.optical, bg.parameters.ns, check.probes, compute.affinities, compute.affinities2, compute.affinities.local, compute.affinity.coef, fast.bkg, gcrma, gcrma.bg.transformation, gcrma.bg.transformation.fast, gcrma.engine, gcrma.engine2, getCDF, getProbePackage, just.gcrma, justGCRMA, left.sigma, mem.bkg, PAV, plotBaseProfiles, GSB.adj

Package: genArise
Exports: a.arise, alter.unique, analysis.window, annotations, back.gui, bg.correct, create.project, cys.plot, filter.spot, genArise, genArise.init, genMerge, get.values, get.Zscore, global.norm, graphic.choose, grid.norm, help, i.arise, imageLimma, m.arise, ma.plot, make.swap, meanUnique, note, old.project, post.analysis, principal, projects.select, r.arise, read.dataset, read.spot, reset.history, ri.plot, set.grid.properties, set.history.project, set.path.project, set.project.properties, single.norm, spotUnique, swap.select, trim, write.dataSet, write.spot, write.zscore, Zscore, Zscore.plot, Zscore.points
ExportClasses: Spot, DataSet

Package: gene2pathway
Exports: retrain, retrain.signaltrans, gene2pathway, gene2pathway.signaltrans, getComponents, get.elements.by.pathway, color.pathway.by.elements, ORF2Entrez, Entrez2ORF, test.overrepresentation

Package: geneRecommender
Exports: gr.cv, gr.main, gr.normalize

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, GenomeIntervals
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: genoset
Exports: BAFSet, baf, lrr, baf<-, lrr<-, BAFSet.to.ExpressionSets, baf2mbaf, CNSet, cn, cn<-, colMeans, GenoSet, locData, locData<-, chr, pos, uniqueChrs, orderedChrs, chrInfo, chrIndices, genoPos, genoPlot, subsetAssayData, genomeAxis, gcCorrect, modeCenter, segs2Rle, segs2RleDataFrame, segTable, runCBS, boundingIndices2, boundingIndices, rangeSampleMeans, chrOrder, isGenomeOrder, genomeOrder
ExportMethods: show, [[, [, elementLengths, ranges, names, universe<-, universe, featureNames<-
ExportClasses: GenoSet, CNSet, BAFSet

Package: girafe
Exports: AlignedGenomeIntervals, plotAligned, trimAdapter, perWindow, fracOverlap, intPhred, coverageOneStrand, addNBSignificance, plotNegBinomFit, medianByPosition, agiFromBam, getFeatureCounts, countReadsAnnotated, chrlengths, clusters, coerce, organism, plot, sample
ExportMethods: plot, [, interval_overlap, interval_included, chrlengths, chrlengths<-, chromosome, coerce, coverage, clusters, detail, export, extend, hist, nchar, matches, matches<-, id, id<-, organism, organism<-, reads, reads<-, reduce, sample, score, score<-, seq_name, show, sort, strand, strand<-, subset, 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, gtConcept, comparative, focusLevel, inheritance, covariates, features, subjects, gt.options, findFocus, getFocus, makeGOstructure, gtPS, gtK, gtI, bbase, repdes, getPS, getK
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, contractedProfile

Package: goseq
Exports: getgo, getlength, goseq, makespline, nullp, plotPWF

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, edgeSetUnion0, extractFromTo, subsetEdgeSets, extractGraphAM, extractGraphBAM, mgEdgeData, mgEdgeData<-
ExportMethods: DFS, Dist, acc, addEdge, addNode, adj, clearNode, clusteringCoefficient, combineNodes, complement, connComp, degree, dumpGXL, edgeL, edgeMatrix, edgeNames, edgeWeights, edgemode, edgemode<-, edges, nodes<-, fromGXL, inEdges, initialize, intersection, intersection2, isAdjacent, isConnected, isDirected, join, nodes, numNodes, numEdges, removeEdge, removeNode, show, subGraph, threshold, toGXL, union, validateGXL, coerce, toDotR, attrDefaults, attrDefaults<-, edgeDataDefaults, edgeDataDefaults<-, mgEdgeDataDefaults, mgEdgeDataDefaults<-, nodeDataDefaults, nodeDataDefaults<-, edgeData, edgeData<-, nodeData, nodeData<-, attrDataItem, attrDataItem<-, removeAttrDataItem<-, ugraph, leaves, updateGraph, extractFromTo, graphIntersect, graphUnion, removeEdgesByWeight, edgeSets
ExportClasses: distGraph, clusterGraph, graph, graphNEL, file, connection, gzfile, bzfile, url, graphAM, attrData, simpleEdge, edgeSet, edgeSetNEL, edgeSetAM, multiGraph, renderInfo, MultiGraph, graphBAM, graphBase

Package: 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, activeWorkflow, activeFlowset, activeNodeID, activeNodeName, getNewName, isAnyActive

Package: iSeq
Exports: iSeq1, iSeq2, peakreg, mergetag, plotreg

Package: idiogram
Exports: .usedChromExprs, .rwb
ExportClasses: cytoband

Package: imageHTS
Exports: parseImageConf, segmentWells, extractFeatures, readLearnTS, predictCellLabels, summarizeWells, segmentATH, getCellFtrsATH, segmentYeastBF, segmentRing, installWebQuery, popWebQuery, installCellPicker, popCellPicker, makeCellHTS, fileHTS, readHTS, parseDCF, collectCellFeatures, getWellFeatures, getUnames, prw2uname, uname2prw, rowcol2well, well2rowcol, well2wellid, zprime, highlightSegmentation, countObjects, getImageConf
ExportClasses: imageHTS

Package: impute
Exports: impute.knn

Package: inveRsion
Exports: setUpGenoDatFile, setUpGenoDatSNPmat, codeHaplo, ROIGenoDat, manual, scanInv
ExportMethods: accBic, getClassif, getInv, getROIs, initialize, listInv, plot, show
ExportClasses: accuracy, GenoDat, GenoDatROI, HaploCode, inversion, inversionList, scan

Package: iterativeBMA
Exports: BssWssFast, bma.predict, brier.score, imageplot.iterate.bma, iterateBMAglm.train, iterateBMAglm.train.predict, iterateBMAglm.train.predict.test, iterateBMAglm.wrapper

Package: iterativeBMAsurv
Exports: assignRiskGroup, crossVal, crossVal.final.calc, crossVal.fold, crossVal.init, crossVal.run, crossVal.tabulate, imageplot.bma.mod, imageplot.iterate.bma.surv, iterateBMAinit, iterateBMAsurv.train, iterateBMAsurv.train.predict.assess, iterateBMAsurv.train.wrapper, predictBicSurv, predictiveAssessCategory, printTopGenes, singleGeneCoxph

Package: joda
Exports: differential.probs, regulation.scores, deregulation.scores, deregulation.p.values

Package: keggorthology
Exports: getKOprobes, indRender, keggDF2graph, getKOtags

Package: lapmix
Exports: lapmix.Fit, laptopTable, lap.volcanoplot

Package: les
Exports: triangWeight, rectangWeight, gaussWeight, epWeight
ExportMethods: plot, show, summary, threshold, regions, ci, export, estimate, chi2, Les
ExportClasses: Les

Package: limma
ExportMethods: show
ExportClasses: RGList, MAList, EListRaw, EList, MArrayLM, TestResults, LargeDataObject, Roast

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.approxPval, vim.permInput, vim.permSNP, vim.permSet

Package: logitT
Exports: logitTAffy

Package: lol
Exports: lasso, matrixLasso, plotGW, lasso.cv, lasso.stability, lasso.simultaneous, lasso.multiSplit, lmMatrixFit, getLambdaNcoef, print.lol, print.lolMatrix
ExportClasses: lol, lolMatrix

Package: lumi
Exports: IlluminaID2nuID, addControlData2lumi, addNuID2lumi, addNuId2lumi, bgAdjust, detectOutlier, detectionCall, estimateLumiCV, getChipInfo, getControlData, getControlProbe, getControlType, getNuIDMappingInfo, id2seq, inverseVST, is.nuID, lumiB, lumiExpresso, lumiN, lumiQ, lumiR, lumiR.batch, lumiT, nuID2EntrezID, nuID2IlluminaID, nuID2RefSeqID, nuID2probeID, nuID2targetID, plotCDF, plotControlData, plotDensity, plotHousekeepingGene, plotSampleRelation, plotStringencyGene, plotVST, probeID2nuID, produceGEOPlatformFile, produceGEOSampleInfoTemplate, produceGEOSubmissionFile, rsn, seq2id, ssn, targetID2nuID, vst, rankinvariant, addControlData2methyLumiM, adjColorBias.quantile, adjColorBias.ssn, addColorChannelInfo, beta2m, bgAdjustMethylation, boxplotColorBias, colorBiasSummary, estimateBeta, estimateM, estimateIntensity, estimateMethylationBG, lumiMethyB, lumiMethyC, lumiMethyN, lumiMethyR, m2beta, normalizeMethylation.quantile, normalizeMethylation.ssn, plotColorBias2D, plotColorBias1D, smoothQuantileNormalization, lumiMethyStatus, gammaFitEM, methylationCall, plotGammaFit
ExportMethods: beadNum, beadNum<-, boxplot, combine, density, detection, detection<-, getHistory, hist, MAplot, pairs, plot, sampleNames, sampleNames<-, exprs, exprs<-, se.exprs, se.exprs<-, show, summary, [, coerce
ExportClasses: LumiBatch

Package: mBPCR
Exports: logAdd, indexLA0, estGlobParam, computeLA0Vect, computeA10, computeRecursions, computeRegrCurve, computePCReg, computeMBPCR, writeEstProfile, importCNData, estProfileWithMBPCR, estProfileWithMBPCRforOligoSnpSet, plotEstProfile

Package: maCorrPlot
Exports: CIrho, CorrSample, CutCI, panel.corr.sample, plot.corr.sample, RandPairs

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, prettyDend, print.comparelists, randomiser, rotate3d, sumstats, suppl, topgenes, s.var, s.groups

Package: maigesPack
Exports: activeMod, activeModScoreHTML, activeNet, activeNetScoreHTML, addGeneGrps, addPaths, bootstrapCor, bootstrapMI, bootstrapT, calcA, calcW, classifyKNN, classifyKNNsc, classifyLDA, classifyLDAsc, classifySVM, classifySVMsc, compCorr, contrastsFitM, createMaigesRaw, createTDMS, deGenes2by2BootT, deGenes2by2Ttest, deGenes2by2Wilcox, deGenesANOVA, designANOVA, getLabels, heatmapsM, hierMde, hierM, kmeansMde, kmeansM, loadData, MI, normLoc, normOLIN, normRepLoess, normScaleLimma, normScaleMarray, plotGenePair, relNet2TGF, relNetworkB, relNetworkM, robustCorr, selSpots, somMde, somM, summarizeReplicates, tableClass, tablesDE
ExportMethods: coerce, show, [
ExportClasses: maigesPreRaw, maigesRaw, maiges, maigesANOVA, maigesDE, maigesDEcluster, maigesClass, maigesRelNetM, maigesRelNetB, maigesActMod, maigesActNet

Package: makecdfenv
Exports: getInfoInFile, make.cdf.env, make.cdf.package, pmormm, read.cdffile
ExportMethods: name.levels<-, name.levels, pbase.levels<-, pbase.levels, pbase<-, pbase, show, tbase.levels<-, tbase.levels, tbase<-, tbase
ExportClasses: Cdf

Package: 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: mcaGUI
Exports: mcaGUI, pmg.gw, pmg.add, pmg.addMenubar, pmg.eval, pmgRepeatTrials, plotecdf, kurtosis, cluster, richness, diversityfun, principle_component, bootstrap, skewness

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, estimateM
ExportMethods: getHistory, betas, pvals, exprs, summary, show, combine, hist, boxplot, pairs, [, QCdata, plotSampleIntensities, qcplot, methylated, unmethylated, unmethylated<-, methylated<-, QCdata<-, exprs<-, pvals<-, betas<-, controlTypes, corplot, controlData, controlData<-, detection, detection<-, methylated.N, methylated.N<-, unmethylated.N, unmethylated.N<-, featureFilter, varFilter
ExportClasses: MethyLumiSet, MethyLumiQC, MethyLumi, MethyLumiM

Package: mgsa
Exports: readGAF
ExportMethods: mgsa, subMgsaSets, itemIndices, length, setAnnotations, itemAnnotations, plot, show, setsMcmcPost, pMcmcPost, betaMcmcPost, alphaMcmcPost, restarts, steps, setsResults, pPost, betaPost, alphaPost, studySetSizeInPopulation, populationSize
ExportClasses: MgsaSets, MgsaMcmcResults, MgsaResults, MgsaGoSets

Package: miRNApath
ExportMethods: show
ExportClasses: mirnapath

Package: microRNA
Exports: get_selfhyb_subseq, show_selfhyb_counts, show_selfhyb_lengths, seedRegions, matchSeeds, RNA2DNA

Package: minet
Exports: aracne, build.mim, clr, fscores, minet, mrnet, mrnetb, pr, rates, show.pr, show.roc, auc.pr, auc.roc, validate

Package: mosaics
Exports: readBins, mosaicsFit, mosaicsPeak, show, print, plot, estimates, export

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: netresponse
Exports: detect.responses, find.similar.features, get.model.parameters, order.responses, read.sif, response2sample, sample2response, model.stats, vdp.mixt, P.rS, P.r.s, P.rs.joint.individual, P.rs.joint, P.Sr, P.S, P.sr, P.s.individual, ICMg.combined.sampler, ICMg.links.sampler, ICMg.get.comp.memberships
ExportMethods: [[, show, get.subnets, get.qofz
ExportClasses: NetResponseModel

Package: nnNorm
Exports: maNormNN, detectSpatialBias, compNorm

Package: nudge
Exports: norm1a, norm1b, norm1c, norm1d, norm2c, norm2d, nudge1, nudge2

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, basicPLM, crlmm, snprma, justSNPRMA, justCRLMM, getPD, plotM, fitPLM, NUSE, RLE
ExportMethods: image, paCalls, intensity, probesetNames, 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, runDate, getNetAffx
ExportClasses: PLMset

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, i2p, p2i, annotationPackages, addFeatureAnnotation, checkExists
ExportMethods: batchStatistics, batchStatistics<-, nu, phi, batch, batchNames, batchNames<-, coerce, flags, 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, A, B, A<-, B<-
ExportClasses: ff_matrix, ffdf, 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: panp
Exports: pa.calls

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: phenoDist
Exports: distToNeg, repDistRank, ctlSeparatn, clusterDist, enrichAnalysis, repCorr, PDMByWellAvg, PDMByFactorAnalysis, PDMByKS, PDMBySvmWeightVector, PDMBySvmAccuracy

Package: phenoTest
Exports: summary.gseaSignificanceSign, summary.gseaSignificanceVar, plot.gseaSignaturesSign, plot.gseaSignaturesVar, ExpressionPhenoTest, epheno2html, heatmapPhenoTest, ClusterPhenoTest, htmlpage, smoothCoxph
ExportMethods: gseaSignatures, gseaSignificance, getEs, getEsSim, getFcHr, dim, phenoNames, p.adjust.method, phenoClass, show, getMeans, getPvals, getSummaryDif, getFc, getHr, logFcHr, export2CSV, [, barplotSignatures, barplotSignifSignatures, pAdjust, getVars2test
ExportClasses: epheno, gseaSignatures, gseaSignaturesSign, gseaSignaturesVar, gseaSignificanceSign, gseaSignificanceVar

Package: pickgene
Exports: adjustlevel, chen.poly, chipnorm, dencont, dencum, denlines, do.oddsplot, em.ggb, fitgg, gammaden, holms, lod.ggb, lod.plot, lodprobes, loglik, makecont, model.pickgene, multipickgene, nlminb, nloglik, normal.richmond, npdiag, nploglik, oddsplot, orangene, pickedchisq, pickedhist, pickedpair, pickedscore, pickgene, pickgene.poly, pickgene.two, pickgene2, pmarg, predrecur, rangene, rankgene, robustbox, robustscale, s.check0, s.check1, s.check2, s.marg, shrinkplot, sixden, toprankgene, twoarray.norm, twoarray.plot, twowayanovapickgene

Package: pint
Exports: iterative.window, fixed.window, fit.cgh.mir.byname, fit.cgh.mrna.byname, pint.data, pint.match, plot.GeneDependencyModel, plot.ChromosomeModels, plot.GenomeModels, screen.cgh.mrna, screen.cgh.mir, W.effects, z.effects
ExportMethods: [[, [[<-, setLoc<-, setGeneName<-, setArm<-, setChromosome<-, getW, getPhi, getScore, getLoc, getGeneName, getChromosome, getArm, getModelMethod, getParams, getPArm, getQArm, getWindowSize, getModelNumbers, topGenes, topModels, orderGenes, findModel, isEmpty, as.data.frame
ExportClasses: GeneDependencyModel, ChromosomeModels, GenomeModels

Package: pkgDepTools
Exports: getInstallOrder, makeDepGraph

Package: plateCore
Exports: panel.densityplot.flowPlate, prepanel.densityplot.flowPlate, prepanel.xyplot.flowPlate, panel.xyplot.flowPlate
ExportMethods: compensate, flowPlate, fixAutoFl, plateSet, phenoData, getGroups, wellAnnotation, Subset, %on%, applyControlGates, summaryStats, sampleNames, fpbind, setControlGates, plotPlate, gutterPlot, mfiPlot, densityplot, xyplot
ExportClasses: flowPlate

Package: plier
Exports: justPlier

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: procoil
Exports: readCCModel
ExportMethods: predict, show, plot, weights, profile
ExportClasses: CCModel, CCProfile

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, qpUpdateCliquesRemoving, qpIPF, qpPAC, qpPCC, qpRndGraph, qpRndWishart, qpG2Sigma, qpUnifRndAssociation, qpK2ParCor, qpPrecisionRecall, qpPRscoreThreshold, qpImportNrr, qpTopPairs, qpPlotNetwork, qpCov, qpRndHMGM, qpSampleFromHMGM
ExportMethods: qpNrr, qpAvgNrr, qpGenNrr, qpPAC, qpPCC, qpCItest, qpEdgeNrr, qpFunctionalCoherence

Package: qrqc
Exports: readSeqFile, plotQuals, plotBases, plotSeqLengths, plotGC, makeReport

Package: quantsmooth
Exports: quantsmooth, quantsmooth.seg, quantsmooth.cv, getLambdaMin, plotSmoothed, getChangedRegions, getChangedIdx, numericCHR, characterCHR, scaleto, plotChromosome, prepareGenomePlot, paintCytobands, lengthChromosome, drawSimpleChrom, position2Cytoband, grid.chromosome

Package: qvalue
Exports: plot.qvalue, qplot, qsummary, qvalue, qvalue.gui, qwrite, summary.qvalue

Package: rGADEM
Exports: GADEM, readPWMfile
ExportMethods: dim, names, consensus, parameters, 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, values, GenomicRanges, GenomicData, GenomicSelection, IRanges, score, score<-, as.data.frame, space, ucscGenomes, BigWigSelection, GRangesForUCSCGenome, GRangesForBSGenome
ExportMethods: activeView, activeView<-, blocks, browseGenome, browserSession, browserSession<-, browserView, browserViews, close, export, export.bed, export.bed15, export.bedGraph, export.gff, export.gff1, export.gff2, export.gff3, export.ucsc, export.wig, export.bw, import, import.bed, import.bed15, import.bedGraph, import.gff, import.gff1, import.gff2, import.gff3, import.ucsc, import.wig, import.bw, import.chain, sequence<-, track<-, track, trackNames, trackNames<-, getTable, tableNames, trackName, trackName<-, tableName, tableName<-, ucscTrackModes, ucscTrackModes<-, ucscSchema, coerce, initialize, show, [, ucscTableQuery, genome, genome<-, chrom, chrom<-, range, range<-, visible, visible<-, liftOver, offset, reversed, nrow, formatDescription, start, end, start<-, end<-, score, score<-, as.data.frame, space, strand
ExportClasses: connection, file, url, gzfile, unz, pipe, sockconn, terminal, characterORconnection, BrowserSession, BrowserView, BrowserViewList, UCSCSession, UCSCView, UCSCData, TrackLine, BasicTrackLine, GraphTrackLine, Bed15TrackLine, UCSCTrackModes, BigWigSelection, UCSCSchema

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: sagenhaft
Exports: combine.libs, compare.lib.pair, compute.sequence.neighbors, compute.unique.tags, create.matrix.csr, difference.scatter.plot, em.estimate.error.given, estimate.errors.mean, extract.ditags, extract.lib.from.directory, extract.lib.from.zip, extract.library.tags, plot.sage.library, plot.sage.library.comparison, print.sage.library, print.sage.library.comparison, read.phd.file, read.sage.library, read.sage.library.comparison, read.seq.qual.filepair, reestimate.lib.from.tagcounts, remove.sage.artifacts, revcomp, sage.test, sagelibrary.simulate, summary.sage.library, summary.sage.library.comparison, table.sparse, tagmatrix2tagnum, tagnum2tagmatrix, tagnum2tagsequence, tagsequence2tagnum, write.sage.library, write.sage.library.comparison

Package: 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, find.a0, fudge2, help.ebam, help.finda0, help.sam, link.genes, link.siggenes, list.siggenes, pi0.est, plotArguments, sam, sam2excel, sam2html, sam.plot2, d.stat, cat.stat, wilc.stat, z.ebam, cat.ebam, wilc.ebam, z.find, denspr, rowWilcoxon, rowRanksWilc, na.handling, nclass.wand, findDelta, qvalue.cal, chisqClass, chisq.ebam, chisq.stat, trend.stat, trend.ebam, md.plot, limma2sam, limma2ebam, samControl, ebamControl, fuzzy.stat, fuzzy.ebam
ExportMethods: show, print, plot, summary, identify
ExportClasses: SAM, EBAM, FindA0, sumSAM, sumEBAM

Package: 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: snm
Exports: snm, sim.singleChannel, sim.doubleChannel, sim.preProcessed, sim.refDesign

Package: snpMatrix
Exports: epsout.ld.snp, filter.rules, Fst, 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, wtccc.sample.list, 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: snpStats
Exports: can.impute, convert.snpMatrix, convert.snpMatrix.dir, filter.rules, Fst, glm.test.control, impute.snps, imputation.maf, imputation.r2, imputation.nsnp, ld, misinherits, mvtests, plotUncertainty, pool, qq.chisq, read.beagle, read.impute, read.mach, read.pedfile, read.plink, read.snps.long, row.summary, col.summary, single.snp.tests, snp.cbind, snp.rbind, snp.cor, snp.imputation, snp.lhs.tests, snp.lhs.estimates, snp.post.multiply, snp.pre.multiply, snp.rhs.tests, snp.rhs.estimates, tdt.snp, test.allele.switch, write.plink, write.SnpMatrix, xxt
ExportMethods: cbind2, chi.squared, deg.freedom, effect.sign, is.na, names, pool2, p.value, rbind2, show, summary, switch.alleles, plot, sample.size, effective.sample.size, [, [<-, coerce, initialize
ExportClasses: SnpMatrix, XSnpMatrix, ImputationRules, SingleSnpTests, SingleSnpTestsScore, GlmTests, GlmEstimates

Package: spikeLI
Exports: collapse, Ivsc, IvsDG

Package: spkTools
Exports: plotSpkBox, spkAccSD, spkAll, spkAnova, spkBal, spkBox, spkDensity, spkGNN, spkMA, spkPair, spkPairNS, spkPot, spkQuantile, spkSlope, spkVar, summarySpkBox
ExportMethods: initialize, spikeIn, spkSplit
ExportClasses: SpikeInExpressionSet

Package: 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: stepNorm
Exports: aov2Dfit, calcAIC, calcBIC, calcEnp, fit2DWithin, fitWithin, loess2Dfit, loessfit, maCompPlate2, makeStepList, medfit, MedianSmooth, noFit, rlm2Dfit, rlmfit, seqWithinNorm, spatialMedfit, square, stepWithinNorm, withinNorm
ExportClasses: marrayFit

Package: tilingArray
Exports: normalizeByReference, segment, costMatrix, findSegments, sampleStep, readCel2eSet, posMin, otherStrand, plotAlongChrom, plotAlongChromLegend, plotSegmentationHeatmap, plotSegmentationDots, plotFeatures, comparisonPlot, plotPenLL, qcPlots, PMindex, BGindex, segChrom, residuals.breakpointsPretend, breakpoints.breakpointsPretend
ExportMethods: plot, show, confint, logLik
ExportClasses: segmentation

Package: timecourse
Exports: abs2ratio, matrix.cov, mb.1D, mb.2D, mb.long, mb.MANOVA, mb.paired, ot.helmert, plotProfile, univ.func
ExportClasses: MArrayTC, LargeDataObject

Package: tkWidgets
Exports: DPExplorer, args2XML, argsWidget, dataViewer, dbArgsWidget, eExplorer, fileBrowser, fileWizard, find.type, guess.header, guess.sep, importPhenoData, importWizard, listSelect, objViewer, objectBrowser, pExplorer, pickItems, tkMIAME, tkSampleNames, tkphenoData, vExplorer, viewVignette, WLValue<-, WName, WRButtons, values.Widget, WValue, WValue<-, WbuttonFun, WbuttonText, WcanEdit, WfromText, WpostFun, WpreFun, WtoText, WwList, WwList<-, print.Widget, WLValue, WEnd, appendSepDir, getWvalues, hasChar, stdType, objNameToList, getPkgContents, getFileContents, pickFiles, pickObjs, print.pWidget, hasPrefix, hasSuffix, hasChar, formatArg
ExportClasses: colInfo

Package: topGO
Exports: annFUN.db, annFUN, annFUN.gene2GO, annFUN.GO2genes, annFUN.org, annFUN.file, combineResults, readMappings, inverseList, whichAlgorithms, whichTests, GOplot, showSigOfNodes, getPvalues, showGroupDensity, reverseArch, nodesInInducedGraph, inducedGraph, buildLevels, getNoOfLevels, getGraphRoot, permSumStats, permSumStats.all, groupGOTerms, .genesInNode, .countsInNode
ExportMethods: initialize, description, ontology, allGenes, feasible, graph, geneSelectionFun, description<-, ontology<-, feasible<-, graph<-, geneSelectionFun<-, print, show, updateGenes, genes, numGenes, geneScore, sigGenes, numSigGenes, usedGO, attrInTerm, genesInTerm, scoresInTerm, countGenesInTerm, termStat, updateTerm<-, allMembers, Name, members, testStatistic, Name<-, allMembers<-, members<-, numMembers, numAllMembers, runTest, sigMembers<-, sigAllMembers, numSigAll, sigMembers, numSigMembers, contTable, allScore, membersScore, score<-, rankMembers, pType, pType<-, membersExpr, getSigGroups, elim, cutOff, elim<-, cutOff<-, updateGroup, Weights<-, Weights, sigRatio<-, getSigRatio, score, testName, algorithm, geneData, geneData<-, score<-, testName<-, algorithm<-, printGenes, penalise, scoreOrder, testStatPar, printGraph, GenTable, GOFisherTest, GOKSTest, GOtTest, GOglobalTest, GOSumTest, GOKSTiesTest, joinFun, allParents, depth, depth<-, expressionMatrix, phenotype
ExportClasses: topGOdata, topGOresult, groupStats, classicCount, classicScore, classicExpr, weight01Count, weight01Score, weight01Expr, elimCount, elimScore, elimExpr, leaCount, leaScore, leaExpr, weightCount, pC, parentChild

Package: tspair
Exports: ts.pair, tspcalc, tspsig, tspplot

Package: twilight
Exports: plot.twilight, print.twilight, twilight, twilight.combi, twilight.filtering, twilight.getlambda, twilight.getmatrix, twilight.permute.pair, twilight.permute.unpair, twilight.pval, twilight.teststat

Package: 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: webbioc
Exports: installReps, mt.wrapper

Package: widgetTools
Exports: button, checkButton, dropdownList, entryBox, env<-, funs, funs<-, label, listBox, makeViewer, oneVScrList, pWidgets, getListOption, pWidgets<-, postFun, postFuns<-, preFun, preFuns<-, radioButton, textBox, tooltip, widget, writeList, writeText, vName, vName<-, wEnv, wEnv<-, wFuns, wFuns<-, wHeight, wHeight<-, wName, wName<-, wNotify, wNotify<-, wPostFun, wPostFun<-, wPreFun, wPreFun<-, wTitle, wTitle<-, wType, wType<-, wValue, wValue<-, wView, wView<-, safeFileOpen, widgetView, getListValue, getTextValue, getEntryValue
ExportClasses: basicPW, widget, widgetView

Package: xcms
Exports: etg, medianFilter, retexp, specNoise, specPeaks, SSgauss, xcmsRaw, xcmsSet, xcmsFragments, xcmsPapply
ExportMethods: absent, calibrate, collect, deepCopy, filepaths, filepaths<-, diffreport, findMZ, findneutral, 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, stitch, write.cdf, write.mzdata
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, trma, bgcorrect, normalize, summarize, express, qualify, bgcorrect.mas4, bgcorrect.mas5, bgcorrect.rma, bgcorrect.gc, normalize.constant, normalize.quantiles, normalize.lowess, normalize.supsmu, summarize.mas4, summarize.mas5, summarize.rma, qualify.rlm, fitQC, fitRLM, rmaPLM, AffyRNAdeg, summaryAffyRNAdeg, plotAffyRNAdeg, boxplot.dev, image.dev, mvaplot.dev, prefilter, unifilter, plotImage, plotBoxplot, 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, borderplot, borders, coiplot, qualOption, qualOption<-, qualType, qualType<-, residuals, weights, xpsRNAdeg, attachCall, attachPVal, pvalData, pvalData<-, presCall, presCall<-, removeCall, removePVal, validCall, validPVal, callplot, attachExpr, corplot, exprs, exprs<-, exprType, exprType<-, madplot, mvaplot, normType, normType<-, nuseplot, pcaplot, rleplot, removeExpr, se.exprs, validExpr, validSE, xpsPreFilter, xpsUniFilter, addData, attachBgrd, attachInten, background, background<-, bgtreeNames, intensity, intensity<-, mm, pm, pmplot, rawCELName, removeBgrd, removeInten, validBgrd, xpsBgCorrect, xpsDABGCall, xpsFIRMA, xpsINICall, xpsMAS4, xpsMAS5, xpsMAS5Call, xpsNormalize, xpsPreprocess, xpsQualify, xpsQualityControl, xpsSummarize, xpsRMA, boxplot, getTreeData, hist, image, 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<-, treeInfo, treeNames, arrayInfo, arrayInfo<-, authorInfo, authorInfo<-, biopsyInfo, biopsyInfo<-, cellineInfo, cellineInfo<-, datasetInfo, datasetInfo<-, hybridizInfo, hybridizInfo<-, primcellInfo, primcellInfo<-, projectInfo, projectInfo<-, sampleInfo, sampleInfo<-, show, sourceInfo, sourceInfo<-, tissueInfo, tissueInfo<-, treatmentInfo, treatmentInfo<-
ExportClasses: ProjectInfo, TreeSet, Filter, PreFilter, UniFilter, SchemeTreeSet, ProcesSet, DataTreeSet, ExprTreeSet, CallTreeSet, FilterTreeSet, AnalysisTreeSet

Package: 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