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: ABAEnrichment Exports: aba_enrich, get_expression, plot_expression, get_name, get_sampled_substructures, get_superstructures, get_annotated_genes, get_id 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: abseqR Exports: abseqReport, report ExportMethods: + ExportClasses: AbSeqRep, AbSeqCRep Package: ABSSeq Exports: LevelstoNormFC<-, counts<-, excounts<-, groups<-, maxRates<-, minRates<-, minimalDispersion<-, normMethod<-, paired<-, sFactors<-, ABSDataSet, ABSSeq, ABSSeqlm, LevelstoNormFC, ReplaceOutliersByMAD, aFoldcomplexDesign, callDEs, callParameter, callParameterwithoutReplicates, counts, estimateSizeFactorsForMatrix, excounts, genAFold, groups, maxRates, minRates, minimalDispersion, normMethod, normalFactors, paired, plotDifftoBase, qtotalNormalized, results, sFactors ExportMethods: sFactors, results, paired, normMethod, minimalDispersion, minRates, maxRates, groups, excounts, counts, LevelstoNormFC, sFactors<-, paired<-, normMethod<-, minimalDispersion<-, minRates<-, maxRates<-, groups<-, excounts<-, counts<-, LevelstoNormFC<- Package: acde Exports: stp, tc, ac, ac2, fdr, bcaFDR, qval Package: ACE Exports: runACE, ploidyplotloop, singlemodel, squaremodel, singleplot, analyzegenomiclocations, getadjustedsegments, objectsampletotemplate, linkvariants, postanalysisloop, twosamplecompare, ACEcall, squaremodelsummary, loopsquaremodel, templatefromequalsegments, segmentstotemplate, compresstemplate, correlationmatrix, correlationmatrixadjusted, forcesegmentsontemplate Package: ACME Exports: do.aGFF.calc, findRegions, read.resultsGFF, findClosestGene, write.bedGraph, write.sgr, getRefflat ExportMethods: show, print, plot, vals, threshold, cutpoints, chromosome, start, end ExportClasses: aGFF, aGFFCalc, ACMESet, ACMECalcSet Package: ADaCGH2 Exports: pSegmentDNAcopy, pSegmentWavelets, pSegmentHMM, pSegmentBioHMM, pSegmentGLAD, pSegmentCGHseg, pSegmentHaarSeg, pChromPlot, inputToADaCGH, outputToCGHregions, cutFile Package: ADAM Exports: ADAnalysis, GFAGAnalysis Package: ADAMgui Exports: GFAGpathUi, GFAGtargetUi Package: adductomicsR Exports: IsotopicDistributionMod, loessWrapperMod, digestMod, findPeaks, adductQuant, filterAdductTable, generateTargTable, outputPeakTable, rtDevModelling, specSimPepId ExportMethods: c ExportClasses: AdductSpec, AdductQuantif Package: adSplit Exports: adSplit, diana2means, drawRandomPS, randomDiana2means, makeEID2PROBESenv Package: AffiXcan Exports: affiXcanBs, affiXcanGReX, affiXcanImpute, affiXcanPca, affiXcanPcs, affiXcanTrain, assoc2list, computeBs, computeCorrelation, computeExpr, computePca, computePcs, computeRSquared, overlookRegions, subsetKFold Package: affy Exports: .setAffyOptions ExportMethods: show, boxplot, image, exprs, exprs<-, featureNames, geneNames, sampleNames, se.exprs, updateObject ExportClasses: AffyBatch Package: affycomp Exports: affycomp, affycomp.compfig2, affycomp.compfig2b, affycomp.compfig3, affycomp.compfig4a, affycomp.compfig4b, affycomp.compfig4c, affycomp.compfig5a, affycomp.compfig5b, affycomp.compfig5c, affycomp.compfig5cde, affycomp.compfig5d, affycomp.compfig5e, affycomp.compfig7, affycomp.compfigs, affycomp.compfigs.calls, affycomp.figure1, affycomp.figure1b, affycomp.figure2, affycomp.figure2b, affycomp.figure3, affycomp.figure4a, affycomp.figure4b, affycomp.figure4c, affycomp.figure5a, affycomp.figure5b, affycomp.figure5c, affycomp.figure5d, affycomp.figure5e, affycomp.figure6a, affycomp.figure6b, affycomp.figure7, affycomp.figure.calls, affycomp.figures, affycompPlot, affycompTable, assessAll, assessDilution, assessFC, assessFC2, assessLS, assessMA, assessMA2, assessSD, assessSignal, assessSpikeIn, assessSpikeIn2, assessSpikeInSD, exprset.log, read.dilution, read.newspikein, read.spikein, remove.hgu133a.xhyb, tableAll, tableDilution, tableFC, tableFC2, tableLS, tableMA2, tableOverallSNR, tableRanks, tableSD, tableSignal, tableSpikeInSD Package: AffyCompatible ExportMethods: show Package: affyContam Exports: setCircRegion, setRectRegion, getCircRegion, getRectRegion Package: affycoretools Exports: affyLinks, affystart, annotateEset, doGlimma, ensemblLinks, entrezLinks, getMainProbes, goLinks, makeGoTable, makeHmap, makeImages, makeVenn, maplot, mirna2mrna, nuccoreLinks, outputRomer, plotDeg, plotHist, plotPCA, runRomer, vennCounts2, vennInLine, vennPage, vennSelect2, writeFit ExportMethods: runRomer, plotPCA, makeVenn, annotateEset Package: AffyExpress Exports: AffyInteraction, AffyQA, AffyRegress, Filter, interaction.result2html, make.contrast, make.design, post.interaction, pre.process, regress, result2html, select.sig.gene, import.data Package: affyPara Exports: distributeFiles, removeDistributedFiles, read.affybatchPara, splitAffyBatch, splitFileVector, splitMatrix, bgCorrectPara, normalizeAffyBatchQuantilesPara, normalizeAffyBatchInvariantsetPara, normalizeAffyBatchConstantPara, normalizeAffyBatchLoessPara, normalizeAffyBatchLoessIterPara, vsn2Para, justvsnPara, vsnrmaPara, computeExprSetPara, preproPara, rmaPara, mergeAffyBatches, combineMatrices, boxplotPara, MAplotPara, MAplotSer, summaryM1M2Para, makeCluster, stopCluster Package: affyPLM ExportClasses: PLMset Package: affyQCReport Exports: affyQAReport, borderQC1, borderQC2, correlationPlot, openQAReport, QCReport, rmQAReport, signalDist, titlePage Package: AffyRNADegradation Exports: RNADegradation, PlotTongs, GetTongs, PlotDegradationHooks ExportMethods: plotDx, d, afbatch ExportClasses: AffyDegradationBatch Package: AGDEX Exports: make.dex.set.object, agdex, write.agdex.result, read.agdex.result, agdex.scatterplot, get.gset.result.details, read.agdex.gset.details, write.agdex.gset.details Package: agilp Exports: AAProcess, AALoess, Baseline, Equaliser, filenamex, Loader, IDswop Package: AgiMicroRna Exports: readMicroRnaAFE, readTargets, qcPlots, boxplotMicroRna, plotDensityMicroRna, RleMicroRna, mvaMicroRna, mvaBASIC, hierclusMicroRna, HeatMapMicroRna, PCAplotMicroRna, cvArray, tgsMicroRna, tgsNormalization, rmaMicroRna, filterMicroRna, esetMicroRna, writeEset, basicLimma, getDecideTests, pvalHistogram, significantMicroRna ExportMethods: show ExportClasses: uRNAList Package: ALDEx2 Exports: aldex ExportMethods: getMonteCarloInstances, getSampleIDs, getFeatures, numFeatures, numMCInstances, getFeatureNames, getReads, numConditions, getMonteCarloReplicate, getMonteCarloSample, getDenom Package: alevinQC Exports: alevinQCReport, alevinQCShiny, checkAlevinInputFiles, plotAlevinBarcodeCollapse, plotAlevinKneeNbrGenes, plotAlevinKneeRaw, plotAlevinQuant, plotAlevinQuantPairs, readAlevinQC Package: AllelicImbalance Exports: alleleCounts<-, alt<-, aquals<-, genotype<-, mapBias<-, phase<-, ref<-, ASEDAnnotationTrack, ASEsetFromArrays, ASEsetFromBam, ASEsetFromCountList, CoverageDataTrack, DetectedAIFromArray, GAnalysis, RiskVariantFromGRangesAndPhaseArray, alleleCounts, alt, altExist, annotationBarplot, aquals, arank, barplotLatticeCounts, barplotLatticeFraction, basic, countAllelesFromBam, countsPerSample, countsPerSnp, coverageMatrixListFromGAL, decorateWithExons, decorateWithGenes, defaultMapBias, defaultPhase, detectAI, detectedAI_vs_threshold_variable_multigraph_plot, detectedAI_vs_threshold_variable_plot, detectedAI_vs_threshold_variable_summary, fraction, fractionPlotDf, frequency, frequency_vs_threshold_variable_multigraph_plot, frequency_vs_threshold_variable_plot, frequency_vs_threshold_variable_summary, gba, genotype, genotype2phase, getAlleleCounts, getAlleleQuality, getAnnotationDataFrame, getAreaFromGeneNames, getCDSFromAnnotation, getCDSVector, getDefaultMapBiasExpMean, getDefaultMapBiasExpMean3D, getExonsFromAnnotation, getExonsVector, getGenesFromAnnotation, getGenesVector, getSnpIdFromLocation, getTranscriptsFromAnnotation, getTranscriptsVector, hetFilt, impBamGAL, impBamGRL, impBcfGR, impBcfGRL, implodeList.old, legendBarplot, locationplot, lva, lva.internal, makeMaskedFasta, mapBias, mapBiasRef, maternalAllele, minCountFilt, minFreqFilt, multiAllelicFilt, paternalAllele, phase, phase2genotype, phaseArray2phaseMatrix, phaseMatrix2Array, pvalue, randomRef, realCigarPosition.old, realCigarPositions.old, realCigarPositionsList.old, ref, refExist, referenceFrequency, reference_frequency_density_vs_threshold_variable_multigraph_plot, reference_frequency_density_vs_threshold_variable_plot, regionSummary, scanForHeterozygotes, scanForHeterozygotes.old, sumnames, thresholdCountSample, thresholdDeltaFrequency, thresholdFrequency, thresholdPvalue, usedSNPs_vs_threshold_variable_summary ExportMethods: usedSNPs_vs_threshold_variable_summary, thresholdPvalue, thresholdFrequency, thresholdDeltaFrequency, thresholdCountSample, sumnames, scanForHeterozygotes, regionSummary, reference_frequency_density_vs_threshold_variable_plot, reference_frequency_density_vs_threshold_variable_multigraph_plot, referenceFrequency, refExist, refAllele, ref, randomRef, pvalue, plot, phaseMatrix2Array, phaseArray2phaseMatrix, phase2genotype, phase, paternalAllele, multiAllelicFilt, minFreqFilt, minCountFilt, maternalAllele, mapBiasRef, mapBias, makeMaskedFasta, lva.internal, lva, locationplot, inferGenotypes, inferAltAllele, inferAlleles, impBcfGRL, impBcfGR, impBamGAL, hetFilt, glocationplot, getSnpIdFromLocation, getDefaultMapBiasExpMean3D, getDefaultMapBiasExpMean, getAreaFromGeneNames, getAlleleQuality, getAlleleCounts, genotype2phase, genotype, gbarplot, gba, frequency_vs_threshold_variable_summary, frequency_vs_threshold_variable_plot, frequency_vs_threshold_variable_multigraph_plot, frequency, fractionPlotDf, fraction, detectedAI_vs_threshold_variable_summary, detectedAI_vs_threshold_variable_plot, detectedAI_vs_threshold_variable_multigraph_plot, detectAI, defaultPhase, defaultMapBias, coverageMatrixListFromGAL, countsPerSnp, countsPerSample, countAllelesFromBam, chisq.test, binom.test, basic, barplot, arank, aquals, altExist, alt, alleleCounts, ASEsetFromBam, ASEDAnnotationTrack, ref<-, phase<-, mapBias<-, genotype<-, aquals<-, alt<-, alleleCounts<- ExportClasses: RiskVariant, RegionSummary, LinkVariantAlmlof, GlobalAnalysis, DetectedAI, ASEset Package: AlphaBeta Exports: ABneutral, ABneutralSOMA, ABnull, ABselectMM, ABselectMMSOMA, ABselectUU, ABselectUUSOMA, BOOTmodel, FtestRSS, convertDMATRIX, dMatrix, makePHYLO, rc.meth.lvl Package: alpine Exports: buildFragtypes, estimateAbundance, extractAlpine, fitBiasModels, getFragmentWidths, getReadLength, mergeGenes, normalizeDESeq, plotFragLen, plotGC, plotGRL, plotOrder0, plotOrder1, plotOrder2, plotRelPos, predictCoverage, splitGenesAcrossChroms, splitLongGenes Package: ALPS Exports: %>%, get_genomic_annotations, get_variable_regions, merge_GR, multiBigwig_summary, plot_browser_tracks, plot_correlation, plot_enrichments, plot_genomic_annotations, plot_motif_logo, process_homer, process_jaspar, process_meme, process_pfm, process_transfac Package: alsace Exports: splitTimeWindow, mergeTimeWindows, smallComps, removeComps, combineComps, suggestCompCombis, correctPeaks, correctRT, doALS, getTime, getWavelength, findpeaks, fitpeaks, filterPeaks, getAllPeaks, getPeakTable, opa, preprocess, showALSresult Package: AMOUNTAIN Exports: CGPFixSS, CGPFixSSMultiLayer, CGPFixSSTwolayer, EuclideanProjectionENNORM, moduleIdentificationGPFixSS, moduleIdentificationGPFixSSMultilayer, moduleIdentificationGPFixSSTwolayer, multilayernetworkSimulation, networkSimulation, twolayernetworkSimulation Package: amplican Exports: barcodeData<-, experimentData<-, fwdReads<-, fwdReadsType<-, readCounts<-, rveReads<-, rveReadsType<-, unassignedData<-, AlignmentsExperimentSet, amplicanAlign, amplicanConsensus, amplicanFilter, amplicanMap, amplicanNormalize, amplicanOverlap, amplicanPipeline, amplicanPipelineConservative, amplicanReport, amplicanSummarize, amplican_print_reads, assignedCount, barcodeData, cigarsToEvents, comb_along, experimentData, extractEvents, findEOP, findLQR, findPD, fwdReads, fwdReadsType, getEvents, lookupAlignment, metaplot_deletions, metaplot_insertions, metaplot_mismatches, pairToEvents, plot_cuts, plot_deletions, plot_height, plot_heterogeneity, plot_insertions, plot_mismatches, plot_variants, readCounts, rveReads, rveReadsType, unassignedCount, unassignedData, writeAlignments ExportClasses: AlignmentsExperimentSet Package: AnalysisPageServer Exports: add.event, add.event.handler, analysis.link, analysis.page.link, analysis.page.of.current.app, annotate.analysis.page.svg, apache.httpd.conf, appendCustomContent, aps.dataset.divs, aps.one.dataset.div, aps.urlEncode, array.param, bool.param, build.service, check.same.svgs, check.signal, checkPackageInstalled, clear.event.handlers, clearRequestEnv, client.ip, combobox.param, compound.param, config.js, copy.front.end, current.app, custom.body.attr, custom.body.html, custom.html.headers, data.frame.to.json, data.frame.to.list, default.param, default.param.set, dies.ok, embed.APS.dataset, eval.within.time, event.names, file.param, get.APS.libbase.prefix, get.APS.outdir, get.page, getCustomContent, getFilterWidget, getTraceback, has.event, has.page, kill.process, knitAPS, lives.ok, messageSectionName, new.FastRWeb.analysis.page.run, new.analysis.page, new.datanode.array, new.datanode.html, new.datanode.plot, new.datanode.simple, new.datanode.table, new.event.registry, new.filter.widget, new.registry, new.response, new.rook.analysis.page.app, pages, param.set, paramSetToJSON, persistent.param.dependencies, persistent.params, platformIsWindows, protect.rapache.memory, rapache.app.from.registry, register.page, remove.event, reset.APS.outdir, rook.analysis.page.server.landing.page, select.param, service.link, set.APS.libbase.prefix, set.APS.outdir, setFilterWidget, setup.APS.knitr, simple.param, slider.param, startRookAnalysisPageServer, static.analysis.page, static.analysis.page.query.string, test.package, trig.registry, trigger.event, tryKeepConditions, tryKeepTraceback, uniquify.ids.in.svg.files, urlDecode, urlEncode, validate.param.value, vwc.conditions, vwc.error, vwc.error.condition, vwc.error.traceback, vwc.is.error, vwc.messages, vwc.messages.conditions, vwc.messages.tracebacks, vwc.n, vwc.n.messages, vwc.n.warnings, vwc.tracebacks, vwc.value, vwc.warnings, vwc.warnings.conditions, vwc.warnings.tracebacks Package: Anaquin Exports: plotLinear, plotLogistic, plotROC, plotLOD, plotConjoint Package: AneuFinder Exports: Aneufinder, bam2GRanges, bed2GRanges, binReads, blacklist, breakpointColors, clusterByQuality, clusterHMMs, collapseBins, compareMethods, consensusSegments, correctGC, exportCNVs, exportGRanges, exportReadCounts, filterSegments, findCNVs, findCNVs.strandseq, findHotspots, fixedWidthBins, getBreakpoints, getQC, getSCEcoordinates, heatmapAneuploidies, heatmapGenomewide, heatmapGenomewideClusters, importBed, karyotypeMeasures, loadFromFiles, plotHeterogeneity, plot_pca, refineBreakpoints, simulateReads, stateColors, strandColors, subsetByCNVprofile, variableWidthBins Package: ANF Exports: ANF, affinity_matrix, eval_clu, kNN_graph, pod, spectral_clustering Package: animalcules Exports: alpha_div_boxplot, alpha_div_test, counts_to_logcpm, counts_to_relabu, df_char_to_factor, differential_abundance, dimred_pca, dimred_pcoa, dimred_tsne, diversities, diversities_help, diversity_beta_boxplot, diversity_beta_heatmap, diversity_beta_test, do_alpha_div_test, filter_categorize, filter_summary_bottom, filter_summary_top, find_biomarker, find_taxon_mat, find_taxonomy, find_taxonomy_300, gini_simpson, grep_tid, inverse_simpson, is_categorical, is_integer0, is_integer1, mae_pick_organisms, mae_pick_samples, pct2str, percent, read_pathoscope_data, relabu_barplot, relabu_boxplot, relabu_heatmap, run_animalcules, shannon, simpson_index, upsample_counts Package: annaffy Exports: selectorWidget, is.annpkg ExportMethods: colnames, colnames<-, getCSS, getHTML, getTD, getText, getURL, probeids, probeids<-, saveHTML, saveText, show, [, [[ ExportClasses: aafChromLoc, aafChromosome, aafCytoband, aafDescription, aafGenBank, aafGO, aafGOItem, aafIntensity, aafList, aafLocusLink, aafPathway, aafPathwayItem, aafProbe, aafPubMed, aafSigned, aafSymbol, aafTable, aafUniGene Package: annotate Exports: .buildAnnotateOpts, .getIdTag, .getNcbiURL, .handleXML, .efetch, .transformAccession, ACC2homology, accessionToUID, ACCNUMStats, annPkgName, aqListGOIDs, buildChromLocation, buildPubMedAbst, checkArgs, chrCats, compatibleVersions, createLLChrCats, createMAPIncMat, dropECode, filterGOByOntology, findChr4LL, findNeighbors, genbank, getAnnMap, getBoundary, getEG, getEvidence, getGI, getGO, getGOChildren, getGOdesc, getGOOntology, getGOParents, getGOTerm, getGPLNames, getLL, getOntology, getOrgNameNCode, getPMID, getPMInfo, getQueryLink, getSAGEFileInfo, getSAGEGPL, getSEQ, getSYMBOL, getUniqAnnItem, getValidChr, GO2heatmap, GOmnplot, hasGOannote, HGID2homology, homoData, htmlpage, KEGG2heatmap, KEGGmnplot, LL2homology, lookUp, makeAnchor, mapOrgs, p2LL, pm.abstGrep, pm.getabst, pm.titles, pmAbst2HTML, pmid2MIAME, PMIDAmat, pmidQuery, probesByLL, pubmed, PWAmat, readGEOAnn, readIDNAcc, readUrl, serializeDataPkgEnvs, serializeEnv, UniGeneQuery, entrezGeneByID, entrezGeneQuery, usedChromGenes, usedChromGenes, weightByConfi, whatACC, setRepository, getRepositories, clearRepository, isValidKey, allValidKeys, updateSymbolsToValidKeys, blastSequences ExportMethods: abstText, articleTitle, authors, chromInfo, chromLengths, chromLocs, chromNames, dataSource, Definition, fileName, geneSymbols, GOID, homoACC, homoHGID, homoLL, homoOrg, homoPS, homoType, homoURL, initialize, journal, mainPage, nChrom, Ontology, organism, pageText, pageTitle, pmid, probesToChrom, pubDate, pubMedAbst, Secondary, show, sidePage, Synonym, Term, toFile, topPage ExportClasses: chromLocation, FramedHTMLPage, homoData, HTMLPage, pubMedAbst Package: AnnotationDbi Exports: unlist2, showQCData, debugSQL, dbGetTable, GOTerms, makeGOGraph, dbFileConnect, dbFileDisconnect, mergeToNamespaceAndExport, getOrgPkgForSchema, chooseCentralOrgPkgSymbol, mapIds_base, resort_base, testForValidKeytype, testSelectArgs, loadDb, createAnnObjs.SchemaChoice, NCBICHIP_DB_SeedGenerator, filterSeeds, checkMAPCOUNTS, make_eg_to_go_map, make_go_to_eg_map, toSQLStringSet, inpIDMapper, intraIDMapper, idConverter, metadata, createSimpleBimap, as.list.Bimap, as.data.frame.Bimap ExportMethods: dbconn, dbfile, taxonomyId, dbmeta, dbschema, dbInfo, direction, direction<-, revmap, colnames, colmetanames, Lkeyname, Rkeyname, keyname, tagname, Rattribnames, Rattribnames<-, Lkeys, Rkeys, keys, Lkeys<-, Rkeys<-, keys<-, subset, [, Llength, Rlength, length, isNA, mappedLkeys, mappedRkeys, mappedkeys, count.mappedLkeys, count.mappedRkeys, count.mappedkeys, show, summary, toTable, as.data.frame, head, tail, nrow, links, count.links, nhit, ncol, dim, toggleProbes, hasMultiProbes, hasSingleProbes, getBimapFilters, setInpBimapFilter, GOID, Term, Ontology, Synonym, Secondary, Definition, GOFrame, GOAllFrame, getGOFrameData, KEGGFrame, getKEGGFrameData, as.list, as.character, ls, mget, eapply, get, exists, [[, $, contents, sample, initialize, saveDb, species, columns, keytypes, select, mapIds, orgPackageName ExportClasses: Bimap, FlatBimap, AnnObj, AnnDbObj, L2Rlink, AnnDbBimap, GoAnnDbBimap, Go3AnnDbBimap, GOTermsAnnDbBimap, AnnDbMap, IpiAnnDbMap, AgiAnnDbMap, ProbeAnnDbBimap, ProbeAnnDbMap, ProbeIpiAnnDbMap, ProbeGo3AnnDbBimap, AnnotationDb, OrgDb, ChipDb, InparanoidDb, GODb, ReactomeDb, GOTerms, GOFrame, GOAllFrame, KEGGFrame Package: AnnotationFilter Exports: AnnotationFilter, AnnotationFilterList, CdsEndFilter, CdsStartFilter, EntrezFilter, ExonEndFilter, ExonIdFilter, ExonNameFilter, ExonRankFilter, ExonStartFilter, GRangesFilter, GeneBiotypeFilter, GeneEndFilter, GeneIdFilter, GeneNameFilter, GeneStartFilter, GenenameFilter, ProteinIdFilter, SeqNameFilter, SeqStrandFilter, SymbolFilter, TxBiotypeFilter, TxEndFilter, TxIdFilter, TxNameFilter, TxStartFilter, UniprotFilter, feature, logicOp, not ExportMethods: value, supportedFilters, show, not, field, distributeNegation, convertFilter, condition ExportClasses: UniprotFilter, TxStartFilter, TxNameFilter, TxIdFilter, TxEndFilter, TxBiotypeFilter, SymbolFilter, SeqStrandFilter, SeqNameFilter, ProteinIdFilter, IntegerFilter, GenenameFilter, GeneStartFilter, GeneNameFilter, GeneIdFilter, GeneEndFilter, GeneBiotypeFilter, GRangesFilter, ExonStartFilter, ExonRankFilter, ExonNameFilter, ExonIdFilter, ExonEndFilter, EntrezFilter, DoubleFilter, CharacterFilter, CdsStartFilter, CdsEndFilter, AnnotationFilterList, AnnotationFilter Package: AnnotationForge Exports: loadAnnDbPkgIndex, makeAnnDbPkg, populateDB, makeDBPackage, available.db0pkgs, available.dbschemas, available.chipdbschemas, wrapBaseDBPackages, makeOrgPackageFromNCBI, makeOrgPackage, makeChipPackage, getProbeDataAffy, getProbeData_1lq, makeProbePackage, makeInpDb ExportMethods: makeAnnDbPkg ExportClasses: AnnDbPkgSeed Package: AnnotationFuncs Exports: translate, pickRefSeq, pickRefSeq.Protein, pickRefSeq.mRNA, mapLists, removeNAs, pickGO, getEvidenceCodes, getOrthologs Package: AnnotationHub Exports: cache, cache<-, query, hubUrl, hubCache, hubDate, snapshotDate, snapshotDate<-, getHub, listResources, loadResources, package, convertHub, isLocalHub, isLocalHub<-, getInfoOnIds, .Hub, AnnotationHub, display, removeCache, getAnnotationHubOption, setAnnotationHubOption, possibleDates, mcols, .httr_proxy, .hub_option_key, .db_close, recordStatus, DispatchClassList, refreshHub, .DollarNames.Hub, as.list.Hub ExportMethods: cache, cache<-, query, hubUrl, hubCache, hubDate, snapshotDate, snapshotDate<-, getHub, isLocalHub, isLocalHub<-, getInfoOnIds, names, length, $, [, subset, [[, as.list, c, show, fileName, display, mcols, dbconn, dbfile ExportClasses: Hub, AnnotationHub, AnnotationHubResource Package: AnnotationHubData Exports: AnnotationHubMetadata, makeAnnotationHubMetadata, UCSCTrackImportPreparer, flog, upload_to_S3, getImportPreparerClasses, makeAnnotationHubResource, HubMetadataFromJson, toJson, constructSeqInfo, makeEnsemblFastaToAHM, makeEnsemblTwoBitToAHM, ensemblFastaToFaFile, ensemblFastaToTwoBitFile, ahmToJson, newResources, updateResources, deleteResources, pushMetadata, pushResources, makeGencodeFastaToAHM, gencodeFastaToFaFile, makeStandardOrgDbsToAHM, makeStandardTxDbsToAHM, makeNCBIToOrgDbsToAHM, getSpeciesList, validSpecies, suggestSpecies, getValidSourceTypes, checkSpeciesTaxId, validDispatchClass, recipeName, run, runRecipes, hubError, hubError<-, inputFiles, outputFile, metadata, metadata<-, metadataList, metadataTable, annotationHubRoot, sourceUrls ExportMethods: show, recipeName, run, runRecipes, hubError, hubError<-, inputFiles, outputFile, metadata, metadata<-, metadataList, metadataTable, annotationHubRoot, sourceUrls ExportClasses: HubMetadata, AnnotationHubMetadata, ImportPreparer, UCSCTrackImportPreparer, UCSCChainPreparer, Grasp2ImportPreparer, EnsemblGtfImportPreparer, EnsemblFastaImportPreparer, Inparanoid8ImportPreparer, NCBIImportPreparer Package: annotationTools Exports: compactList, getANNOTATION, getGENEID, getGENEONTOLOGY, getGENESYMBOL, getGENETITLE, getHOMOLOG, getMULTIANNOTATION, getOrthologousProbesets, getPROBESET, listToCharacterVector, ps2ps Package: annotatr Exports: annotate_regions, annotatr_cache, build_ah_annots, build_annotations, builtin_annotations, builtin_genomes, plot_annotation, plot_categorical, plot_coannotations, plot_numerical, plot_numerical_coannotations, randomize_regions, read_annotations, read_regions, summarize_annotations, summarize_categorical, summarize_numerical Package: anota Exports: anotaPerformQc, anotaResidOutlierTest, anotaGetSigGenes, anotaPlotSigGenes Package: anota2seq Exports: anota2seqDataSetFromMatrix, anota2seqDataSetFromSE, anota2seqAnalyze, anota2seqRegModes, anota2seqPerformQC, anota2seqSelSigGenes, anota2seqResidOutlierTest, anota2seqRun ExportMethods: anota2seqPlotGenes, anota2seqPlotPvalues, anota2seqPlotFC, anota2seqGetThresholds, anota2seqGetDeltaData, anota2seqGetResidOutlierTest, anota2seqGetQualityControl, anota2seqGetOutput, anota2seqGetContrasts, anota2seqGetCovariates, anota2seqGetNormalizedData Package: antiProfiles Exports: apStats, ev ExportMethods: getProbesetIds, getProbeStats, getNormalTissueRegions, getNormalRegions, buildAntiProfile, apReorder, apCount ExportClasses: TissueSpecAntiProfile, AntiProfileStats, AntiProfile Package: APAlyzer Exports: REF3UTR, PASEXP_3UTR, REFCDS, GENEXP_CDS, PASEXP_IPA, APAdiff Package: apComplex Exports: bhmaxSubgraph, findComplexes, mergeComplexes, plotComplex, sortComplexes Package: apeglm Exports: apeglm, bbEstDisp, logLikNB, svalue Package: appreci8R Exports: appreci8Rshiny, filterTarget, normalize, annotate, combineOutput, evaluateCovAndBQ, determineCharacteristics, finalFiltration Package: ArrayExpress Exports: ArrayExpress, getAE, queryAE, ae2bioc, getcolproc, getcolraw, procset, extract.zip Package: ArrayExpressHTS Exports: ArrayExpressHTS, ArrayExpressHTSFastQ, prepareReference, prepareAnnotation, getPipelineOptions, getPipelineOption, setPipelineOptions, isRCloud, getDefaultProcessingOptions, getDefaultRCloudOptions, getDefaultFilteringOptions Package: arrayMvout ExportMethods: ArrayOutliers, plot, show ExportClasses: arrOutStruct Package: arrayQuality Exports: readAgilent, readcontrolCode, agQuality, EMSplit, getSpikeIds, getSpikeIndex, gpQuality, globalQuality, maQualityPlots, meeboQuality, meeboQualityPlots, heeboQuality, heeboQualityPlots, PRv9mers, PRvQCHyb, qualBoxplot, qualityScore, qcScore, readGPR, readSpikeTypes, readSpot, slideQuality, scaleRefTable, spotQuality, HeeboSpotTypes, MeeboSpotTypes, controlCodeHeebo, controlCodeMeebo Package: arrayQualityMetrics Exports: arrayQualityMetrics, prepdata, prepaffy, aqm.writereport, aqm.boxplot, aqm.maplot, aqm.density, aqm.probesmap, aqm.meansd, aqm.heatmap, aqm.pca, aqm.rle, aqm.nuse, aqm.rnadeg, aqm.pmmm, aqm.spatial, addXYfromGAL, outliers, boxplotOutliers ExportClasses: aqmReportModule, outlierDetection Package: ArrayTools Exports: createExpressionSet, createIndex, geneFilter, regress, postInteraction, createIngenuityFile, output.gct, output.cls, output.ing, createGSEAFiles, adjustment, getAdjP, getDesign, getAnnotation, getCompare1, getCompare2, getContrast, getCovariates, getF, getFC, getFCCutoff, getFilterMethod, getID, getIndex, getInteraction, getIntIndex, getLength, getLevel, getTarget, getNormalizationMethod, getP, getPCutoff, Output2HTML, qa3prime, qaGeneST, regressionMethod, selectSigGene, Sort, preProcessGeneST, preProcess3prime, selectSigGene, selectSigGeneInt ExportMethods: adjustment, getAdjP, getAnnotation, getContrast, getF, getFC, getFCCutoff, getFilterMethod, getID, getIndex, getNormalizationMethod, getP, getPCutoff, Output2HTML, regressionMethod, show, Sort, summary, getLength, getCompare1, getCompare2, getInteraction, getLevel, initialize, getCovariates, getDesign, getIntIndex, getTarget ExportClasses: regressResult, interactionResult, designMatrix, contrastMatrix Package: ARRmNormalization Exports: getDesignInfo, getBackground, getQuantiles, getCoefficients, positionPlots, quantilePlots, normalizeARRm Package: artMS Exports: artmsAnalysisQuantifications, artmsAnnotateSpecie, artmsAnnotationUniprot, artmsAvgIntensityRT, artmsChangeColumnName, artmsConvertMetabolomics, artmsDataPlots, artmsEnrichLog2fc, artmsEnrichProfiler, artmsEvidenceToSAINTq, artmsEvidenceToSaintExpress, artmsFilterEvidenceContaminants, artmsGeneratePhSiteExtended, artmsIsEvidenceNewVersion, artmsIsSpeciesSupported, artmsLeaveOnlyUniprotEntryID, artmsMapUniprot2Entrez, artmsMergeEvidenceAndKeys, artmsMsstatsSummary, artmsPhosfateOutput, artmsPhotonOutput, artmsPlotHeatmapQuant, artmsProtein2SiteConversion, artmsQualityControlEvidenceBasic, artmsQualityControlEvidenceExtended, artmsQualityControlMetabolomics, artmsQualityControlSummaryExtended, artmsQuantification, artmsResultsWide, artmsSILACtoLong, artmsSpectralCounts, artmsVolcanoPlot, artmsWriteConfigYamlFile Package: ASAFE Exports: algorithm_1snp_wrapper, algorithm_1snp Package: ASEB Exports: SequenceInfo, readSequence, asebSites, asebProteins, drawStat, drawEScurve Package: ASGSCA Exports: GSCA, GSCAestim Package: ASICS Exports: ASICS, ASICSUsersGuide, alignSpectra, binning, createPureLibrary, createSpectra, formatForAnalysis, importSpectra, importSpectraBruker, kruskalWallis, normaliseSpectra, oplsda, pca, plotAlignment ExportMethods: summary, show, plot, length, getTypeData, getTypeAnalysis, getSpectra, getSampleName, getResults, getReconstructedSpectra, getQuantification, getPpmGrid, getNormParams, getNormMethod, getNbProtons, getMeanByGroup, getDeformedLibrary, getDataset, getCVError, getBestModel, dim, c, [ ExportClasses: Spectra, PureLibrary, AnalysisResults, ASICSResults Package: ASpediaFI Exports: as.table<-, events<-, gene.table<-, gtf<-, network<-, pathway.table<-, psi<-, samples<-, ASpediaFI, analyzeFI, annotateASevents, as.table, events, exportNetwork, gene.table, gtf, network, pathway.table, psi, quantifyPSI, samples, visualize ExportMethods: samples, psi, pathway.table, network, gtf, gene.table, events, as.table, samples<-, psi<-, pathway.table<-, network<-, gtf<-, gene.table<-, events<-, as.table<- ExportClasses: ASpediaFI Package: ASpli ExportMethods: AsDiscover, binGenome, DUreport, writeAS, writeCounts, writeDU, writeRds, rds, readCounts, featuresg, featuresb, featuresj, countsg, countsb, countsj, countse1i, countsie2, rdsg, rdsb, irPIR, altPSI, esPSI, joint, junctionsPIR, junctionsPSI, genesDE, binsDU, junctionsDU, DUreportBinSplice, show, junctionDUreport, containsGenesAndBins, containsJunctions, plotBins, plotGenomicRegions, subset, mergeBinDUAS, filterDU ExportClasses: ASpliAS, ASpliCounts, ASpliDU, ASpliFeatures Package: AssessORF Exports: AssessGenes, CompareAssessmentResults, MapAssessmentData, ScoreAssessmentResults Package: ASSET Exports: h.traits, h.types, h.summary, h.forestPlot, z.max, p.dlm, p.tube Package: ASSIGN Exports: ComBat.step2, assign.convergence, assign.cv.output, assign.mcmc, assign.output, assign.preprocess, assign.summary, assign.wrapper, gather_assign_results, merge_drop, optimizeGFRN, pcaplot, runassignGFRN Package: ATACseqQC Exports: NFRscore, PTscore, TSSEscore, bamQC, distanceDyad, enrichedFragments, estimateLibComplexity, factorFootprints, footprintsScanner, fragSizeDist, plotCorrelation, plotFootprints, prepareBindingSitesList, readBamFile, readsDupFreq, saturationPlot, shiftGAlignmentsList, splitBam, splitGAlignmentsByCut, vPlot, writeListOfGAlignments Package: atSNP Exports: ComputeMotifScore, ComputePValues, GetIUPACSequence, LoadFastaData, LoadMotifLibrary, LoadSNPData, MatchSubsequence, dtMotifMatch, plotMotifMatch Package: attract Exports: filterDataSet, findAttractors, removeFlatGenes, findSynexprs, plotsynexprs, findCorrPartners, calcFuncSynexprs ExportClasses: SynExpressionSet, AttractorModuleSet Package: AUCell Exports: AUCell_buildRankings, AUCell_calcAUC, AUCell_createViewerApp, AUCell_exploreThresholds, AUCell_plotHist, AUCell_plotTSNE, aucellResults, getAUC, getAssignments, getRanking, getThresholdSelected, nGenes, orderAUC, plotGeneCount, plotTsne_cellProps, setGeneSetNames, subsetGeneSets, updateAucellResults ExportMethods: getRanking, getAUC, cbind Package: Autotuner Exports: EICparams, ThresholdingAlgo, createAutotuner, getAutoFactorCol, getAutoFile_col, getAutoFile_paths, getAutoIntensity, getAutoMetadata, getAutoPeak_difference, getAutoPeak_table, getAutoPeaks, getAutoTime, isolatePeaks, plot_peaks, plot_signals, returnParams, setAutoFactorCol, setAutoFile_col, setAutoFile_paths, setAutoIntensity, setAutoMetadata, setAutoPeak_difference, setAutoPeak_table, setAutoPeaks, setAutoTime ExportClasses: Autotuner Package: AWFisher Exports: AWFisher_pvalue, biomarkerCategorization, function_edgeR, function_limma, variabilityIndex Package: BaalChIP Exports: BaalChIP ExportMethods: summaryQC, summaryASB, plotSimul, plotQC, mergePerGroup, getASB, filterIntbias, filter1allele, alleleCounts, adjustmentBaalPlot, QCfilter, BaalChIP.run, BaalChIP.report, BaalChIP.get Package: bacon Exports: bacon, dnormmix, plotnormmix, rnormmix ExportMethods: tstat, traces, topTable, se, pval, posteriors, plot, meta, inflation, fit, estimates, es, bias Package: BADER Exports: BADER Package: BadRegionFinder Exports: determineCoverage, determineCoverageQuality, determineRegionsOfInterest, reportBadRegionsSummary, reportBadRegionsDetailed, reportBadRegionsGenes, plotSummary, plotDetailed, plotSummaryGenes, determineQuantiles Package: BAGS Exports: DataGeneSets, Gibbs5, Gibbs4, Gibbs3, Gibbs2, MCMCDataSet, ReadGMT Package: ballgown Exports: expr<-, indexes<-, pData<-, annotate_assembly, ballgown, ballgownrsem, checkAssembledTx, clusterTranscripts, collapseTranscripts, contains, dirs, eexpr, expr, exprfilter, geneIDs, geneNames, getAttributeField, getGenes, gexpr, gffRead, gffReadGR, iexpr, indexes, last, mergedDate, pData, pctOverlap, plotLatentTranscripts, plotMeans, plotTranscripts, sampleNames, seqnames, stattest, structure, subset, tGene, texpr, transcriptIDs, transcriptNames, writeFiles ExportMethods: transcriptNames, transcriptIDs, texpr, subset, structure, seqnames, sampleNames, pData, mergedDate, indexes, iexpr, gexpr, geneNames, geneIDs, expr, eexpr, dirs, pData<-, indexes<-, expr<- ExportClasses: ballgown Package: bamsignals Exports: alignSignals, bamCount, bamCoverage, bamProfile ExportMethods: width, length, bamProfile, bamCoverage, bamCount, as.list, alignSignals, [ ExportClasses: CountSignals Package: BANDITS Exports: create_data, eff_len_compute, filter_genes, filter_transcripts, plot_precision, prior_precision, test_DTU ExportMethods: transcript, top_transcripts, top_genes, show, plot_proportions, gene, convergence ExportClasses: BANDITS_test, BANDITS_data Package: banocc Exports: banocc_model, get_banocc_output, run_banocc Package: basecallQC Exports: basecallQC, createBCLcommand, createBasemasks, demuxBarplot, demuxBoxplot, indexlengths.bcl2fastqparams, makeFQTable, passFilterBar, passFilterBoxplot, passFilterTilePlot, readlengths.bcl2fastqparams, reportBCL, BCL2FastQparams, summaryConvStatsTable, summaryDemuxTable, validateBCLSheet, baseCallMetrics, demultiplexMetrics, interOpsReport ExportMethods: readlengths, indexlengths ExportClasses: basecallQC, BCL2FastQparams Package: BaseSpaceR Exports: ServiceURI, ResponseStatus, AppAuth, performOAuth, authWebClient, authNativeClient, uri, initializeAuth, requestAccessToken, hasAccess, Id, Name, Href, DateCreated, UserOwnedBy, Status, HrefBaseSpaceUI, Items, DisplayedCount, TotalCount, Offset, Limit, SortDir, SortBy, auth, Users, userItem, Runs, listRuns, runItem, runCollection, Projects, listProjects, projectItem, projectCollection, createProject, Samples, listSamples, sampleItem, sampleCollection, AppResults, appResultItem, appResultCollection, listAppResults, createAppResults, AppSessions, listAppSessions, updateAppSessions, Genomes, listGenomes, genomeItem, genomeCollection, Files, listFiles, fileItem, fileCollection, getFiles, putFiles, getIndexedBam, getBAMs, countRuns, countProjects, countSamples, countAppResults, countAppSessions, countGenomes, countFiles, getVariantSet, getVariants, getCoverage, getCoverageStats ExportMethods: uri, initializeAuth, requestAccessToken, hasAccess, Id, Name, Href, DateCreated, UserOwnedBy, Status, HrefBaseSpaceUI, Items, DisplayedCount, TotalCount, Offset, Limit, SortDir, SortBy, auth, Users, Runs, listRuns, Projects, listProjects, createProject, Samples, listSamples, AppResults, listAppResults, createAppResults, AppSessions, listAppSessions, updateAppSessions, Genomes, listGenomes, Files, listFiles, getFiles, putFiles, getBAMs, countRuns, countProjects, countSamples, countAppResults, countAppSessions, countGenomes, countFiles, getVariantSet, getVariants, getCoverage, getCoverageStats, $, show, as.list ExportClasses: ServiceURI, ResponseStatus, AppAuth, AppSessionAuth, Item, Collection, Response, Users, userItem, Runs, RunsSummary, runItem, runCollection, Genomes, GenomesSummary, genomeItem, genomeCollection, Projects, ProjectsSummary, projectItem, projectCollection, Samples, SamplesSummary, sampleItem, sampleCollection, AppResults, AppResultsSummary, appResultItem, appResultCollection, AppSessions, appSessionItem, Files, FilesSummary, fileItem, fileCollection Package: Basic4Cseq ExportMethods: prepare4CseqData, createVirtualFragmentLibrary, printBEDFragmentLibrary, checkRestrictionEnzymeSequence, giveEnzymeSequence, readPointsOfInterestFile, readsToFragments, chooseNearCisFragments, normalizeFragmentData, getReadDistribution, visualizeViewpoint, drawHeatmap, exportVisualizationFragmentData, importVisualizationFragmentData, printWigFile, simulateDigestion, drawDigestionFragmentHistogram, plotTransInteractions, Data4Cseq, viewpointChromosome, viewpointChromosome<-, viewpointInterval, viewpointInterval<-, readLength, readLength<-, pointsOfInterest, pointsOfInterest<-, rawReads, rawReads<-, rawFragments, rawFragments<-, nearCisFragments, nearCisFragments<- ExportClasses: Data4Cseq Package: BASiCS Exports: BASiCS_CorrectOffset, BASiCS_D_TestDE, BASiCS_DenoisedCounts, BASiCS_DenoisedRates, BASiCS_DetectHVG, BASiCS_DetectLVG, BASiCS_DiagHist, BASiCS_DiagPlot, BASiCS_EffectiveSize, BASiCS_Filter, BASiCS_LoadChain, BASiCS_MCMC, BASiCS_ShowFit, BASiCS_Sim, BASiCS_TestDE, BASiCS_VarThresholdSearchHVG, BASiCS_VarThresholdSearchLVG, BASiCS_VarianceDecomp, BASiCS_diagHist, BASiCS_diagPlot, BASiCS_effectiveSize, BASiCS_showFit, makeExampleBASiCS_Data, newBASiCS_Chain, newBASiCS_Data ExportMethods: updateObject, subset, show, rownames, plot, displaySummaryBASiCS, displayChainBASiCS, colnames, Summary ExportClasses: BASiCS_Summary, BASiCS_Chain Package: BasicSTARRseq ExportMethods: getPeaks, sample, sample<-, control, control<- ExportClasses: STARRseqData Package: batchelor Exports: ClassicMnnParam, FastMnnParam, NoCorrectParam, RegressParam, RescaleParam, batchCorrect, checkBatchConsistency, checkIfSCE, checkRestrictions, correctExperiments, cosineNorm, divideIntoBatches, fastMNN, findMutualNN, mnnCorrect, multiBatchNorm, multiBatchPCA, noCorrect, reducedMNN, regressBatches, rescaleBatches ExportMethods: batchCorrect ExportClasses: RescaleParam, RegressParam, NoCorrectParam, FastMnnParam, ClassicMnnParam, BatchelorParam Package: BatchQC Exports: batchQC, batchQC_analyze, batchQC_condition_adjusted, batchQC_filter_genes, batchQC_fsva_adjusted, batchQC_num.sv, batchQC_shapeVariation, batchQC_sva, batchQC_svregress_adjusted, batchqc_circosplot, batchqc_correlation, batchqc_corscatter, batchqc_explained_variation, batchqc_heatmap, batchqc_pc_explained_variation, batchqc_pca, batchqc_pca_svd, batchtest, combatPlot, getShinyInput, getShinyInputCombat, getShinyInputOrig, getShinyInputSVA, getShinyInputSVAf, getShinyInputSVAr, gnormalize, lmFitC, log2CPM, plot_genewise_moments, plot_samplewise_moments, rnaseq_sim, setShinyInput, setShinyInputCombat, setShinyInputOrig, setShinyInputSVA, setShinyInputSVAf, setShinyInputSVAr ExportClasses: BatchQCout Package: BayesKnockdown Exports: BayesKnockdown, BayesKnockdown.diffExp, BayesKnockdown.es Package: BayesPeak Exports: bayespeak, summarise.peaks, summarize.peaks, read.bed, plot.overfitdiag, identify.overfitdiag, region.overfitdiag, plot.bed, plot.job, plot.PP Package: bayNorm Exports: AdjustSIZE_fun, BB_Fun, BetaFun, DownSampling, EstPrior, NOISY_FUN, Prior_fun, SyntheticControl, bayNorm, bayNorm_sup, noisy_gene_detection Package: baySeq ExportClasses: countData Package: BBCAnalyzer Exports: analyzeBases, analyzeBasesPlotOnly Package: BCRANK Exports: bcrank, matchingSites ExportMethods: show, toptable, fname, searchPath, pwm, plot, bcrankScore, consensus, matchVector ExportClasses: BCRANKmatch, BCRANKsearch, BCRANKresult Package: bcSeq Exports: bcSeq_hamming, bcSeq_edit, trimRead, uniqueBar Package: BDMMAcorrect Exports: BDMMA, fdr_cut, trace_plot, VBatch Package: beadarray Exports: insertBeadData, removeBeadData, getBeadData, plotChipLayout, createTargetsFile, quickSummary, summarize, identifyControlBeads, insertSectionData, backgroundCorrectSingleSection, beadarrayUsersGuide, suggestAnnotation, addFeatureData, readIllumina, readLocsFile, convertBeadLevelList, readIdatFiles, processSwathData, readTIFF, plotTIFF, illuminaForeground, illuminaBackground, illuminaSharpen, medianBackground, logGreenChannelTransform, logRedChannelTransform, logRatioTransform, greenChannelTransform, redChannelTransform, greenChannel, plotBeadIntensities, genericBeadIntensityPlot, poscontPlot, outlierplot, imageplot, checkRegistration, makeQCTable, expressionQCPipeline, calculateOutlierStats, controlProbeDetection, plotBeadLocations, makeControlProfile, combinedControlPlot, BASH, HULK, generateNeighbours, BASHCompact, BASHDiffuse, BASHExtended, setWeights, showArrayMask, readBeadSummaryData, normaliseIllumina, medianNormalise, calculateDetection, checkPlatform, getAnnotation, setAnnotation, beadStatusVector, plotMAXY, illuminaOutlierMethod, squeezedVarOutlierMethod, weightsOutlierMethod, noOutlierMethod, readSampleSheet, makeGEOSubmissionFiles, createGEOMeta, createGEOMatrix, limmaDE ExportMethods: metrics, p95, snr, show, [[, dim, sectionNames, numBeads, boxplot, exprs, se.exprs, nObservations, Detection, annotation, annotation<-, se.exprs<-, exprs<-, nObservations<-, Detection<-, qcData, combine, DesignMatrix, ContrastMatrix, ArrayWeights, LogFC, LogOdds, PValue, ArrayWeights<-, LogFC<-, LogOdds<-, PValue<-, DesignMatrix<-, ContrastMatrix<- ExportClasses: BeadLevelList, beadLevelData, ExpressionSetIllumina, illuminaChannel, beadRegistrationData, limmaResults Package: beadarraySNP Exports: read.SnpSetIllumina, backgroundEstimate, backgroundCorrect.SNP, normalizeBetweenAlleles.SNP, normalizeBetweenSubsamples.SNP, normalizeWithinArrays.SNP, normalizeLoci.SNP, RG2polar, polar2RG, standardNormalization, heterozygousSNPs, compareGenotypes, heterozygosity, reportSamplesSmoothCopyNumber, reportChromosomesSmoothCopyNumber, pdfSamplesSmoothCopyNumber, pdfChromosomesSmoothCopyNumber, removeLowQualityProbes, removeLowQualitySamples, calculateQCarray, pdfQC, smoothed.intensity, renameOPA, calculateLOH, reportGenomeGainLossLOH, pdfChromosomeGainLossLOH, reportChromosomeGainLossLOH, reportGenomeIntensityPlot, convert2aCGH, convert2SegList, segmentate, reportGenotypeSegmentation, plotGoldenGate4OPA, plotGenomePanels, createCNSummary, alterCN, getDNAindex, interactiveCNselect, setRealCN, Sample_Map2Samplesheet, pdfBeadstudioQC, BeadstudioQC, calculateLair, GetBeadStudioSampleNames, dist.GT, calculateSmooth ExportMethods: [, [[, $, annotation, combine, experimentData, exprs, featureNames, pData, phenoData, sampleNames, samples, featureData, sortGenomic, annotation<-, description<-, experimentData<-, exprs<-, featureNames<-, pData<-, phenoData<-, sampleNames<-, assayData<-, featureData<-, fData, fData<-, dim, assayData, initialize, arrayType<-, arrayID<-, arrayType, arrayID, plotQC, reportSamplePanelQC, calculateGSR, cn.segments, cn.segments<- ExportClasses: SnpSetIllumina, SnpSetSegments, QCIllumina Package: BeadDataPackR Exports: decompressBeadData, compressBeadData, readCompressedData, extractLocsFile Package: BEAT Exports: makeParams, positions_to_regions, generate_results, epimutation_calls Package: BEclear Exports: calcBatchEffects, calcScore, calcSummary, clearBEgenes, correctBatchEffect, countValuesToPredict, findOutsideValues, imputeMissingData, localLoss, loss, makeBoxplot, preprocessBEclear, replaceOutsideValues Package: BgeeDB Exports: Bgee, formatData, getAnnotation, getData, listBgeeRelease, listBgeeSpecies, loadTopAnatData, makeTable, topAnat ExportClasses: Bgee Package: BGmix Exports: BGmix, ccSummary, ccTrace, ccParams, ccPred, plotCompare, plotBasic, plotTrace, plotFDR, plotPredChecks, plotMixDensity, calcFDR, TailPP, histTailPP, FDRforTailPP, FDRplotTailPP, EstimatePi0, readBGX Package: bgx Exports: bgx, standalone.bgx, readOutput.bgx, plotExpressionDensity, plotDEDensity, plotDEHistogram, rankByDE, plotDiffRank Package: BHC Exports: bhc, WriteOutClusterLabels, DiscretiseData, FindOptimalBinning Package: BicARE Exports: FLOC, bicluster, testAnnot, testSet, residue, makeReport Package: BiFET Exports: calculate_enrich_p Package: bigmemoryExtras Exports: BigMatrix, BigMatrixFactor, updateBackingfiles, updateBigMatrix ExportMethods: nrow, nlevels, ncol, levels, length, dimnames, dim, as.matrix, apply, levels<-, dimnames<-, [<-, [ ExportClasses: BigMatrixFactor, BigMatrix Package: bigPint Exports: plotClusters, plotLitre, plotLitreApp, plotPCP, plotPCPApp, plotSM, plotSMApp, plotVolcano, plotVolcanoApp Package: bioassayR Exports: connectBioassayDB, addDataSource, loadBioassay, dropBioassay, disconnectBioassayDB, newBioassayDB, addBioassayIndex, dropBioassayIndex, activeTargets, inactiveTargets, activeAgainst, selectiveAgainst, getAssay, getAssays, parsePubChemBioassay, getBioassaySetByCids, perTargetMatrix, targetSelectivity, screenedAtLeast, loadIdMapping, translateTargetId, assaySetTargets, allCids, allTargets, bioactivityFingerprint, scaleBioassaySet, crossReactivityProbability, crossReactivityPrior, trinarySimilarity ExportMethods: queryBioassayDB, show, aid, source_id, assay_type, organism, scoring, targets, target_types, scores, aid<-, source_id<-, assay_type<-, organism<-, scoring<-, targets<-, target_types<-, scores<-, activity, sources, activity<-, sources<- ExportClasses: BioassayDB, bioassay, bioassaySet Package: Biobase Exports: Aggregate, addVigs2WinMenu, anyMissing, as.data.frame.ExpressionSet, assayDataNew, assayDataValidMembers, assayDataElementNames, assayDataElement, assayDataElementReplace, assayDataElement<-, cache, copyEnv, copySubstitute, createPackage, dumpPackTxt, esApply, getPkgVigs, isUnique, listLen, matchpt, mkScalar, multiassign, NChannelSet, note, openPDF, openVignette, package.version, reverseSplit, rowMax, rowMedians, rowMin, rowQ, readExpressionSet, read.AnnotatedDataFrame, read.MIAME, MIAME, selectSome, strbreak, subListExtract, testBioCConnection, lcSuffix, lcPrefix, lcPrefixC, updateOldESet, userQuery, validMsg, write.AnnotatedDataFrame ExportMethods: [, [[, $, abstract, aggenv, aggfun, annotatedDataFrameFrom, annotation, channel, channelNames, coerce, combine, content, contents, description, dimnames, dimnames<-, dims, experimentData, expinfo, exprs, featureNames, featureData, fData, fvarLabels, fvarMetadata, hybridizations, initfun, length, locked, makeDataPackage, normControls, notes, otherInfo, pData, phenoData, preproc, protocolData, sampleNames, samples, se.exprs, selectChannels, snpCall, snpCallProbability, storageMode, varLabels, varMetadata, annotation<-, channelNames<-, description<-, dimLabels<-, experimentData<-, exprs<-, featureNames<-, featureData<-, fData<-, fvarLabels<-, fvarMetadata<-, notes<-, preproc<-, pData<-, phenoData<-, protocolData<-, sampleNames<-, snpCall<-, snpCallProbability<-, varLabels<-, varMetadata<-, assayData<-, se.exprs<-, storageMode<-, write.exprs, dim, dimLabels, assayData, pubMedIds, pubMedIds<-, isVersioned, isCurrent, classVersion, classVersion<-, updateObject, updateObjectTo, initialize, show, Compare, AnnotatedDataFrame, ExpressionSet ExportClasses: aggregator, container, eSet, MIAxE, MIAME, characterORMIAME, annotatedDataset, AssayData, data.frameOrNULL, AnnotatedDataFrame, Versions, VersionsNull, Versioned, VersionedBiobase, ExpressionSet, MultiSet, SnpSet, NChannelSet, ScalarObject, ScalarInteger, ScalarLogical, ScalarNumeric, ScalarCharacter Package: biobroom Exports: augment.DGEList, augment.MArrayLM, augment.deSet, augment.qvalue, augment_sva, glance.DGEExact, glance.GRanges, glance.GRangesList, glance.MArrayLM, glance.deSet, glance.qvalue, glance_sva, tidy.DESeqDataSet, tidy.DESeqResults, tidy.DGEExact, tidy.DGEList, tidy.EList, tidy.ExpressionSet, tidy.GRanges, tidy.GRangesList, tidy.MAList, tidy.MArrayLM, tidy.MSnSet, tidy.RangedSummarizedExperiment, tidy.deSet, tidy.qvalue, tidy_sva Package: bioCancer Exports: Edges_Diseases_obj, Mutation_obj, Node_Diseases_obj, Node_df_FreqIn, Node_obj_CNA_ProfData, Node_obj_FreqIn, Node_obj_Met_ProfData, Node_obj_mRNA_Classifier, Studies_obj, UnifyRowNames, attriColorGene, attriColorValue, attriColorVector, attriShape2Gene, attriShape2Node, bioCancer, checkDimensions, coffeewheel, coffeewheelOutput, displayTable, findPhantom, getFreqMutData, getGenesClassification, getListProfData, getList_Cases, getList_GenProfs, getMegaProfData, getSequensed_SampleSize, grepRef, metabologram, metabologramOutput, reStrColorGene, reStrDimension, reStrDisease, renderCoffeewheel, renderMetabologram, whichGeneList, widgetThumbnail Package: BiocCaseStudies Exports: parseLibVers, requiredPackages, packages2install, resample, mySessionInfo, fixedWidthCat, lcol1, lcol2, lcol3, dcol1, dcol2, dcol3, numName, sepInt Package: BiocCheck Exports: BiocCheck, BiocCheckGitClone, usage, usage2, .error, .warning, .note Package: BiocFileCache Exports: bfcmeta<-, BiocFileCache, bfcadd, bfccache, bfccount, bfcdownload, bfcinfo, bfcmeta, bfcmetalist, bfcmetaremove, bfcneedsupdate, bfcnew, bfcpath, bfcquery, bfcquerycols, bfcremove, bfcrid, bfcrpath, bfcsync, bfcupdate, cleanbfc, exportbfc, importbfc, makeBiocFileCacheFromDataFrame, makeCachedActiveBinding, removebfc ExportMethods: show, removebfc, makeBiocFileCacheFromDataFrame, length, importbfc, exportbfc, cleanbfc, bfcupdate, bfcsync, bfcrpath, bfcrid, bfcremove, bfcquerycols, bfcquery, bfcpath, bfcnew, bfcneedsupdate, bfcmetaremove, bfcmetalist, bfcmeta, bfcinfo, bfcdownload, bfccount, bfccache, bfcadd, bfcmeta<-, [[<-, [[, [ Package: BiocGenerics Exports: append, as.data.frame, as.list, as.vector, cbind, rbind, colSums, rowSums, colMeans, rowMeans, do.call, duplicated, anyDuplicated, eval, evalq, pmax, pmin, pmax.int, pmin.int, Reduce, Filter, Find, Map, Position, get, mget, grep, grepl, is.unsorted, lapply, sapply, mapply, match, %in%, mean, nrow, ncol, NROW, NCOL, order, paste, rank, rep.int, rownames, rownames<-, colnames, colnames<-, union, intersect, setdiff, sort, start, start<-, end, end<-, width, width<-, pos, subset, t, table, tapply, unique, unlist, unsplit, which, which.max, which.min, relist, boxplot, image, density, IQR, mad, residuals, var, sd, weights, xtabs, clusterCall, clusterApply, clusterApplyLB, clusterEvalQ, clusterExport, clusterMap, clusterSplit, parLapply, parSapply, parApply, parRapply, parCapply, parLapplyLB, parSapplyLB, annotation, annotation<-, combine, dbconn, dbfile, dims, fileName, normalize, Ontology, organism, organism<-, species, species<-, path, path<-, basename, basename<-, dirname, dirname<-, plotMA, plotPCA, score, score<-, strand, strand<-, invertStrand, toTable, type, type<-, updateObject, updateObjectFromSlots, getObjectSlots, unstrand ExportMethods: combine, updateObject, counts, counts<-, design, design<-, dispTable, dispTable<-, sizeFactors, sizeFactors<-, conditions, conditions<-, estimateSizeFactors, estimateDispersions, plotDispEsts, plotMA, plotPCA, invertStrand ExportClasses: connection, file, url, gzfile, bzfile, unz, pipe, fifo, sockconn, terminal, textConnection, gzcon, characterORconnection, AsIs, dist Package: biocGraph Exports: imageMap Package: BiocNeighbors Exports: AnnoyIndex, AnnoyIndex_path, AnnoyIndex_search_mult, AnnoyParam, AnnoyParam_directory, AnnoyParam_ntrees, AnnoyParam_search_mult, HnswIndex, HnswIndex_ef_search, HnswIndex_path, HnswParam, HnswParam_directory, HnswParam_ef_construction, HnswParam_ef_search, HnswParam_nlinks, KmknnIndex, KmknnIndex_cluster_centers, KmknnIndex_cluster_info, KmknnParam, KmknnParam_kmeans_args, VptreeIndex, VptreeIndex_nodes, VptreeParam, bndata, bndistance, bnorder, buildAnnoy, buildHnsw, buildIndex, buildKmknn, buildVptree, findAnnoy, findHnsw, findKNN, findKmknn, findNeighbors, findVptree, queryAnnoy, queryHnsw, queryKNN, queryKmknn, queryNeighbors, queryVptree, rangeFindKmknn, rangeFindVptree, rangeQueryKmknn, rangeQueryVptree ExportMethods: show, queryNeighbors, queryKNN, findNeighbors, findKNN, dimnames, dim, buildIndex, bnorder, bndistance, bndata ExportClasses: VptreeParam, VptreeIndex, KmknnParam, KmknnIndex, HnswParam, HnswIndex, BiocNeighborParam, BiocNeighborIndex, AnnoyParam, AnnoyIndex Package: BiocOncoTK Exports: %>%, TcgaMutCounts, TcgaNIndWithAnyMut, bindMSI, bipg_tests, buildPancanSE, clueDemos, clueServiceNames, dbListTables, featIDMapper, filter, get_plates, ggFeatDens, ggFeatureSegs, ggMutDens, loadPatel, load_NRAS_AHR, load_ccleNRAS, load_nrasdf, log10pl1, mc3toGR, multiviz, oncoPrintISB, pancan_BQ, pancan_app, pancan_clinicalTabVarnames, pancan_longname, pancan_tabulate, pertClasses, query_clue, replaceRownames, select, tbl, tumNorSet, viz_msi_raw Package: BioCor Exports: AintoB, D2J, J2D, addSimilarities, clusterGeneSim, clusterSim, combinadic, combineScores, combineScoresPar, combineSources, diceSim, duplicateIndices, geneSim, inverseList, mclusterGeneSim, mclusterSim, mgeneSim, mpathSim, pathSim, removeDup, seq2mat, similarities, weighted.prod, weighted.sum ExportMethods: pathSim, mgeneSim, mclusterSim, mclusterGeneSim, geneSim, clusterSim, clusterGeneSim Package: BiocParallel Exports: MulticoreParam, SnowParam, DoparParam, SerialParam, BatchJobsParam, BatchtoolsParam, register, registered, bpparam, bpnworkers, bptry, bploop, multicoreWorkers, snowWorkers, batchtoolsWorkers, batchtoolsCluster, batchtoolsRegistryargs, batchtoolsTemplate, bpvalidate, bpok, bprunMPIslave, ipcid, ipcremove, ipclock, ipctrylock, ipcunlock, ipclocked, ipcyield, ipcvalue, ipcreset, bplapply, bpvec, bpvectorize, bpmapply, bpaggregate, bpiterate, bpworkers, bpworkers<-, bpbackend, bpbackend<-, bptasks, bptasks<-, bpjobname, bpjobname<-, bpstart, bpstop, bpisup, bpstopOnError, bpstopOnError<-, bpprogressbar, bpprogressbar<-, bpRNGseed, bpRNGseed<-, bptimeout, bptimeout<-, bpexportglobals, bpexportglobals<-, bplog, bplog<-, bplogdir, bplogdir<-, bpthreshold, bpthreshold<-, bpresultdir, bpresultdir<-, bpschedule, .BiocParallelParam_prototype, .prototype_update, .prettyPath, .send_to, .recv_any, .send, .recv, .close, .send_all, .recv_all, .bpstart_impl, .bpstop_impl, .bpworker_impl, .bplapply_impl, .bpiterate_impl, .error_worker_comm ExportMethods: show, bplapply, bpvec, bpvectorize, bpmapply, bpaggregate, bpiterate, bpworkers, bpworkers<-, bpbackend, bpbackend<-, bptasks, bptasks<-, bpjobname, bpjobname<-, bpstart, bpstop, bpisup, bpstopOnError, bpstopOnError<-, bpprogressbar, bpprogressbar<-, bpRNGseed, bpRNGseed<-, bptimeout, bptimeout<-, bplog, bplog<-, bplogdir, bplogdir<-, bpthreshold, bpthreshold<-, bpresultdir, bpresultdir<-, bpschedule ExportClasses: BiocParallelParam, MulticoreParam, SnowParam, DoparParam, SerialParam, BatchJobsParam, BatchtoolsParam Package: BiocPkgTools Exports: biocBuildEmail, biocBuildReport, biocDownloadStats, biocExplore, biocPkgList, buildPkgDependencyDataFrame, buildPkgDependencyIgraph, firstInBioc, getBiocVignette, getPackageInfo, get_bioc_data, githubDetails, githubURLParts, inducedSubgraphByPkgs, problemPage, subgraphByDegree Package: BiocSet Exports: BiocSet, BiocSet_from_elementset, arrange_element, arrange_elementset, arrange_set, data.frame_from_element, data.frame_from_elementset, data.frame_from_set, es_activate, filter_element, filter_elementset, filter_set, go_sets, intersect_single, kegg_sets, left_join_element, left_join_elementset, left_join_set, map_add_element, map_add_set, map_multiple, map_set, map_unique, mutate_element, mutate_elementset, mutate_set, select_element, select_elementset, select_set, summarise_element, summarise_elementset, summarise_set, tibble_from_element, tibble_from_elementset, tibble_from_set, union_single, url_ref, url_ref_element, url_ref_set ExportMethods: import, export, es_set, es_elementset, es_element, coerce ExportClasses: BiocSet Package: BiocSingular Exports: DeferredMatrix, DeferredMatrixSeed, ExactParam, FastAutoParam, IrlbaParam, LowRankMatrix, LowRankMatrixSeed, RandomParam, ResidualMatrix, ResidualMatrixSeed, bsdeferred, bsfold, bsparam, runExactSVD, runIrlbaSVD, runPCA, runRandomSVD, runSVD ExportMethods: tcrossprod, t, show, runSVD, runPCA, rowSums, rowMeans, extract_array, dimnames, dim, crossprod, colSums, colMeans, DelayedArray, dimnames<-, [, %*% ExportClasses: ResidualMatrixSeed, ResidualMatrix, RandomParam, LowRankMatrixSeed, LowRankMatrix, IrlbaParam, FastAutoParam, ExactParam, DeferredMatrixSeed, DeferredMatrix, BiocSingularParam Package: BiocSklearn Exports: H5matref, SklearnEls, getTransformed, h5mat, pyobj, skIncrPCA, skKMeans, skPCA, skPartialPCA_step ExportMethods: skIncrPPCA, pyobj, getTransformed ExportClasses: SkDecomp Package: BiocStyle Exports: Biocannopkg, Biocexptpkg, Biocpkg, CRANpkg, Githubpkg, Rpackage, doc_date, html_document, latex, markdown, md_document, output, pdf_document, pkg_ver Package: biocViews Exports: writeBiocViews, getBiocViews, write_VIEWS, write_REPOSITORY, genReposControlFiles, extractVignettes, extractManuals, extractCitations, getCurrentbiocViews, extractNEWS, extractHTMLDocuments, extractTopLevelFiles, writeRepositoryHtml, writePackageDetailHtml, getSubTerms, getBiocSubViews, validate_bioc_views, writeTopLevelView, writeHtmlDoc, write_SYMBOLS, writeRFilesFromVignettes, getPackageNEWS, printNEWS, recommendBiocViews, recommendPackages, guessPackageType ExportMethods: coerce, show, htmlDoc, htmlValue, htmlFilename ExportClasses: Htmlized, PackageDetail, pdAuthorMaintainerInfo, pdVignetteInfo, pdDownloadInfo, pdDetailsInfo, pdDescriptionInfo, pdVigsAndDownloads, RepositoryDetail, rdPackageTable, BiocView, bvTitle, bvPackageTable, bvSubViews, bvParentViews Package: BiocWorkflowTools Exports: createBiocWorkflow, f1000_article, markdownToLatex, uploadToOverleaf Package: bioDist Exports: cor.dist, spearman.dist, tau.dist, euc, man, mutualInfo, KLdist.matrix, KLD.matrix, closest.top, MIdist ExportMethods: KLD.matrix, KLdist.matrix, cor.dist, euc, man, mutualInfo, MIdist, spearman.dist, tau.dist Package: biomaRt Exports: listMarts, getGene, getSequence, exportFASTA, useMart, listDatasets, useDataset, listEnsembl, useEnsembl, listAttributes, listFilters, getBM, getXML, getLDS, attributePages, filterOptions, filterType, getBMlist, NP2009code, keys, columns, keytypes, select, listEnsemblArchives, searchAttributes, searchDatasets, searchFilters, listFilterValues, searchFilterValues, biomartCacheClear, biomartCacheInfo ExportMethods: show ExportClasses: Mart Package: biomformat Exports: biom, biom_data, biom_shape, header, make_biom, matrix_element_type, observation_metadata, read_biom, read_hdf5_biom, sample_metadata, write_biom ExportMethods: show, rownames, nrow, ncol, colnames ExportClasses: biom Package: BioMM Exports: BioMM, BioMMstage2pred, baseGLMnet, baseModel, baseRandForest, baseSVM, cirPlot4pathway, classifiACC, getDataByFilter, getMetrics, omics2pathlist, plotRankedFeature, plotVarExplained, predByBS, predByCV, predByFS, reconBySupervised, reconByUnsupervised Package: BioMVCClass ExportMethods: ordering, grLayout, rNames, ordering<-, grLayout<-, rNames<-, incidMat, gTestStat, gsTestStat, expData, descr, incidMat<-, gTestStat<-, gsTestStat<-, expData<-, descr<- ExportClasses: graphModel, exprModel, graphView, heatmapView, GSE, gseModel Package: biomvRCNS Exports: biomvRhsmm, hsmmRun, sojournAnno, biomvRseg, regionSegCost, regionSegAlphaNB, biomvRmgmr, maxGapminRun, biomvRGviz, splitFarNeighbour, simSegData ExportMethods: plot, show ExportClasses: biomvRCNS Package: BioNet Exports: saveNetwork, loadNetwork.sif, loadNetwork.tab, rmSelfLoops, makeNetwork, subNetwork, largestComp, largestScoreComp, permutateNodes, compareNetworks, getEdgeList, writeHeinzEdges, writeHeinzNodes, writeHeinz, runHeinz, scanFDR, readHeinzTree, readHeinzGraph, runFastHeinz, mapByVar, plot.bum, hist.bum, plotLLSurface, plotModule, plot3dModule, save3dModule, aggrPvals, fbum, fbumLL, bumOptim, print.bum, summary.bum, fitBumModel, fdrThreshold, piUpper, scoreOffset, scoreFunction, scoreNodes, getCompScores, resamplingPvalues, consensusScores, sortedEdgeList Package: BioNetStat Exports: KLdegree, KLspectrum, adjacencyMatrix, averageBetweennessCentrality, averageBetweennessEdgesCentrality, averageClosenessCentrality, averageClusteringCoefficient, averageDegreeCentrality, averageEigenvectorCentrality, averageShortestPath, betweennessCentrality, betweennessCentralityTest, betweennessCentralityVertexTest, betweennessEdgesCentrality, centralityPathPlot, closenessCentrality, closenessCentralityTest, closenessCentralityVertexTest, clusteringCoefficient, clusteringCoefficientTest, clusteringCoefficientVertexTest, degreeCentrality, degreeCentralityTest, degreeCentralityVertexTest, degreeDistributionTest, diffNetAnalysis, doLabels, edgeBetweennessEdgeTest, edgeBetweennessTest, eigenvectorCentrality, eigenvectorCentralityTest, eigenvectorCentralityVertexTest, nDegreeDensities, nSpectralDensities, pathPlot, readGmtFile, readVarFile, runBioNetStat, spectralDistributionTest, spectralEntropies, spectralEntropyTest Package: BioQC Exports: gsNamespace<-, GmtList, SignedGenesets, SignedIndexList, absLog10p, appendGmtList, as.GmtList, entropy, entropyDiversity, entropySpecificity, filterBySize, filterPmat, gini, gmtlist2signedGenesets, gsDesc, gsGeneCount, gsGenes, gsName, gsNamespace, gsSize, hasNamespace, readGmt, readSignedGmt, sampleSpecialization, setDescAsNamespace, setNamespace, simplifyMatrix, uniqGenesetsByNamespace, wmwTestInR ExportMethods: wmwTest, show, offset, matchGenes, SignedIndexList, IndexList, offset<- ExportClasses: SignedIndexList, SignedGenesets, IndexList, GmtList 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: biosigner Exports: biosign, getAccuracyMN, getSignatureLs ExportMethods: show, predict, plot, getSignatureLs, getMset, getEset, getAccuracyMN, biosign ExportClasses: biosignMultiDataSet, biosign Package: Biostrings Exports: IUPAC_CODE_MAP, mergeIUPACLetters, AMINO_ACID_CODE, AA_ALPHABET, AA_STANDARD, AA_PROTEINOGENIC, GENETIC_CODE, RNA_GENETIC_CODE, GENETIC_CODE_TABLE, getGeneticCode, DNA_BASES, RNA_BASES, DNA_ALPHABET, RNA_ALPHABET, seqtype, seqtype<-, get_seqtype_conversion_lookup, alphabet, xscodes, extract_character_from_XString_by_positions, extract_character_from_XString_by_ranges, make_XString_from_string, BString, DNAString, RNAString, AAString, make_XStringSet_from_strings, BStringSet, DNAStringSet, RNAStringSet, AAStringSet, unmasked, BStringSetList, DNAStringSetList, RNAStringSetList, AAStringSetList, xscat, readBStringSet, readDNAStringSet, readRNAStringSet, readAAStringSet, fasta.index, fasta.seqlengths, fastq.seqlengths, fastq.geometry, writeXStringSet, saveXStringSet, letter, getSeq, letterFrequency, letterFrequencyInSlidingView, alphabetFrequency, hasOnlyBaseLetters, uniqueLetters, consensusMatrix, consensusString, mkAllStrings, oligonucleotideFrequency, dinucleotideFrequency, trinucleotideFrequency, nucleotideFrequencyAt, oligonucleotideTransitions, twoWayAlphabetFrequency, replaceAmbiguities, dinucleotideFrequencyTest, complement, reverseComplement, translate, codons, toComplex, extractAt, replaceAt, replaceLetterAt, .inplaceReplaceLetterAt, injectHardMask, padAndClip, stackStrings, strsplit, N50, width0, startIndex, endIndex, extractAllMatches, neditStartingAt, neditEndingAt, neditAt, isMatchingStartingAt, isMatchingEndingAt, isMatchingAt, which.isMatchingStartingAt, which.isMatchingEndingAt, which.isMatchingAt, hasLetterAt, mismatch, nmatch, nmismatch, gregexpr2, matchPattern, countPattern, vmatchPattern, vcountPattern, maskMotif, mask, matchLRPatterns, trimLRPatterns, matchProbePair, maxWeights, minWeights, maxScore, minScore, unitScale, PWM, PWMscoreStartingAt, matchPWM, countPWM, findPalindromes, palindromeArmLength, palindromeLeftArm, palindromeRightArm, tb, tb.width, nnodes, hasAllFlinks, computeAllFlinks, patternFrequency, PDict, matchPDict, countPDict, whichPDict, vmatchPDict, vcountPDict, vwhichPDict, subpatterns, pattern, PhredQuality, SolexaQuality, IlluminaQuality, encoding, quality, QualityScaledBStringSet, QualityScaledDNAStringSet, QualityScaledRNAStringSet, QualityScaledAAStringSet, readQualityScaledDNAStringSet, writeQualityScaledXStringSet, insertion, deletion, unaligned, aligned, indel, nindel, PairwiseAlignments, alignedPattern, alignedSubject, pid, PairwiseAlignmentsSingleSubject, writePairwiseAlignments, nedit, mismatchTable, mismatchSummary, compareStrings, lcprefix, lcsuffix, pmatchPattern, lcsubstr, nucleotideSubstitutionMatrix, errorSubstitutionMatrices, qualitySubstitutionMatrices, pairwiseAlignment, stringDist, DNAMultipleAlignment, RNAMultipleAlignment, AAMultipleAlignment, rowmask, rowmask<-, colmask, colmask<-, maskGaps, maskednrow, maskedncol, maskeddim, readDNAMultipleAlignment, readRNAMultipleAlignment, readAAMultipleAlignment, consensusViews, write.phylip, detail, needwunsQS, longestConsecutive, matchprobes ExportMethods: length, [, rep, coerce, as.vector, as.character, as.matrix, toString, show, summary, start, end, width, Views, subpatterns, pattern, quality, encoding, insertion, deletion, parallelSlotNames, unaligned, aligned, indel, nindel, parallelVectorNames, subject, type, alignedPattern, alignedSubject, score, pid, PairwiseAlignments, PairwiseAlignmentsSingleSubject, mismatch, nmatch, nmismatch, nedit, mismatchTable, mismatchSummary, coverage, compareStrings, lcprefix, lcsuffix, pmatchPattern, lcsubstr, pairwiseAlignment, stringDist, nchar, names, names<-, [[, windows, consensusMatrix, consensusString, alphabetFrequency, as.list, rowmask, rowmask<-, colmask, colmask<-, maskGaps, maskednrow, maskedncol, maskeddim, consensusViews, needwunsQS, initialize, startIndex, endIndex, unlist, neditStartingAt, neditEndingAt, isMatchingStartingAt, isMatchingEndingAt, matchPattern, countPattern, vcountPattern, maskMotif, matchLRPatterns, trimLRPatterns, matchProbePair, maxWeights, minWeights, maxScore, minScore, PWM, matchPWM, countPWM, findPalindromes, palindromeArmLength, palindromeLeftArm, palindromeRightArm, tb, tb.width, nnodes, hasAllFlinks, computeAllFlinks, head, tail, patternFrequency, PDict, matchPDict, countPDict, whichPDict, vmatchPDict, vcountPDict, vwhichPDict, ==, !=, duplicated, is.unsorted, order, sort, rank, toComplex, letter, substr, substring, letterFrequency, letterFrequencyInSlidingView, hasOnlyBaseLetters, uniqueLetters, oligonucleotideFrequency, nucleotideFrequencyAt, dinucleotideFrequencyTest, chartr, reverse, complement, reverseComplement, codons, translate, extractAt, replaceAt, replaceLetterAt, injectHardMask, strsplit, unstrsplit, seqtype, seqtype<-, updateObject, showAsCell, relistToClass, union, intersect, setdiff, setequal, %in%, match, pcompare, as.data.frame, subseq, threebands, subseq<-, collapse, gaps, unmasked, maskedwidth, maskedratio, masks, masks<- ExportClasses: XStringPartialMatches, XStringQuality, PhredQuality, SolexaQuality, IlluminaQuality, QualityScaledXStringSet, QualityScaledBStringSet, QualityScaledDNAStringSet, QualityScaledRNAStringSet, QualityScaledAAStringSet, InDel, AlignedXStringSet0, AlignedXStringSet, QualityAlignedXStringSet, PairwiseAlignments, PairwiseAlignmentsSingleSubject, PairwiseAlignmentsSingleSubjectSummary, MultipleAlignment, DNAMultipleAlignment, RNAMultipleAlignment, AAMultipleAlignment, MIndex, ByPos_MIndex, PreprocessedTB, Twobit, ACtree2, PDict3Parts, PDict, TB_PDict, MTB_PDict, Expanded_TB_PDict, XString, BString, DNAString, RNAString, AAString, XStringSet, BStringSet, DNAStringSet, RNAStringSet, AAStringSet, XStringViews, MaskedXString, MaskedBString, MaskedDNAString, MaskedRNAString, MaskedAAString, XStringSetList, BStringSetList, DNAStringSetList, RNAStringSetList, AAStringSetList Package: biosvd Exports: assayColorMap<-, contrast<-, featureColorMap<-, figure<-, filenames<-, negativeValues<-, palette<-, path<-, plots<-, prefix<-, whichAssays<-, whichEigenassays<-, whichEigenfeatures<-, whichFeatures<-, whichPolarAxes<-, apply, assayColorMap, assayMatrix, assaycorrelations, colorIdFeatures, contrast, eigenassays, eigenexpressions, eigenfeatures, entropy, excludeEigenfeatures, featureColorMap, featureMatrix, featurecorrelations, figure, filenames, fractions, matrix, negativeValues, palette, path, plots, prefix, signMatrix, whichAssays, whichEigenassays, whichEigenfeatures, whichFeatures, whichPolarAxes ExportMethods: report, project, plot, exclude, compute ExportClasses: EigensystemPlotParam, Eigensystem Package: BioTIP Exports: getBiotypes, getCTS, getCluster_methods, getIc, getMCI, getMaxMCImember, getMaxStats, getNetwork, getReadthrough, optimize.sd_selection, plotBar_MCI, plotIc, plotMaxMCI, plot_Ic_Simulation, plot_MCI_Simulation, plot_simulation_sample, sd_selection, simulationMCI, simulation_Ic Package: biotmle Exports: .biotmle, biomarkertmle, eif, heatmap_ic, modtest_ic, rnaseq_ic, toptable, volcano_ic ExportClasses: data.frame_OR_EList, bioTMLE Package: biovizBase Exports: getBioColor, plotColorLegend, genBrewerBlindPalInfo, genDichromatPalInfo, genBlindPalInfo, colorBlindSafePal, blind.pal.info, brewer.pal.blind.info, dichromat.pal.blind.info, estimateCoverage, transformToCircle, transformToRectInCircle, transformToBarInCircle, transformToSegInCircle, transformToLinkInCircle, transformDfToGr, transformGRangesForEvenSpace, isIdeogram, isSimpleIdeogram, getIdeogram, containLetters, pileupAsGRanges, pileupGRangesAsVariantTable, GCcontent, showColor, isJunctionRead, isMatchedWithModel, flatGrl, getIdeoGR, getScale, getFormalNames, subsetArgsByFormals, parseArgsForAes, parseArgsForNonAes, strip_formula_dots, is_coord_truncate_gaps, is_coord_genome ExportMethods: addStepping, shrinkageFun, maxGap, splitByFacets, getGaps, getXScale, getYLab, getXLab, crunch, mold, transformToGenome, transformToDf Package: BiRewire Exports: birewire.analysis.bipartite, birewire.rewire.undirected, birewire.analysis.undirected, birewire.rewire.bipartite, birewire.bipartite.from.incidence, birewire.similarity, birewire.rewire.bipartite.and.projections, birewire.sampler.bipartite, birewire.sampler.undirected, birewire.visual.monitoring.bipartite, birewire.visual.monitoring.undirected, birewire.sampler.dsg, birewire.rewire.dsg, birewire.induced.bipartite, birewire.build.dsg, birewire.load.dsg, birewire.similarity.dsg, birewire.analysis.dsg, birewire.visual.monitoring.dsg, birewire.slum.to.sparseMatrix Package: birta Exports: birta, get_potential_swaps, limmaAnalysis, plotConvergence Package: biscuiteer Exports: CpGindex, RRBSeq, WGBSage, WGBSeq, atRegions, binCoverage, biscuitMetadata, byChromArm, byExtremality, checkBiscuitBED, condenseSampleNames, extremality, filterLoci, fixAge, fixNAs, getClock, getLogitFracMeth, grToSeg, makeBSseq, readBiscuit, segToGr, simplifySampleNames, summarizeBsSeqOver, unionize ExportMethods: samples, meta, info, header, geno, fixed Package: BitSeq Exports: parseAlignment, estimateExpression, estimateExpressionLegacy, estimateVBExpression, getMeanVariance, estimateHyperPar, estimateDE, getGeneExpression, getWithinGeneExpression, getDE, getExpression, loadSamples, writeSamples Package: blacksheepr Exports: annotationlist_builder, comparison_groupings, count_outliers, create_heatmap, deva, deva_normalization, deva_results, make_comparison_columns, make_outlier_table, outlier_analysis, outlier_heatmap Package: blima Exports: chipArrayStatistics, log2TransformPositive, bacgroundCorrect, writeBackgroundImages, plotBackgroundImageBeforeCorrection, plotBackgroundImageAfterCorrection, nonPositiveCorrect, varianceBeadStabilise, quantileNormalize, doTTests, doProbeTTests, createSummarizedMatrix, backgroundChannelSubtract, selectedChannelTransform, xieBacgroundCorrect Package: BLMA Exports: addCLT, bilevelAnalysisClassic, bilevelAnalysisGene, bilevelAnalysisGeneset, bilevelAnalysisPathway, fisherMethod, intraAnalysisClassic, intraAnalysisGene, loadKEGGPathways, stoufferMethod Package: bnbc Exports: bnbc, ContactGroup, contacts, contacts<-, librarySize, logCPM, boxSmoother, gaussSmoother, getBandMatrix, getGroupZeros, dropGroupZeros, cgBandApply, cgApply, distanceIdx, getBandIdx, band<-, band ExportMethods: rowData, rowData<-, colData, colData<-, dim, show, [ ExportClasses: ContactGroup Package: BPRMeth Exports: betareg_gradient, betareg_log_likelihood, boxplot_cluster_expr, bpr_cluster_wrap, bpr_gradient, bpr_log_likelihood, bpr_optim, bpr_predict_wrap, cluster_profiles_mle, cluster_profiles_vb, create_anno_region, create_fourier_object, create_polynomial_object, create_rbf_object, create_region_object, design_matrix, eval_function, eval_probit_function, impute_bulk_met, infer_profiles_gibbs, infer_profiles_mle, infer_profiles_vb, inner_predict_model_expr, inner_train_model_expr, lr_log_likelihood, old_boxplot_cluster_gex, old_plot_cluster_prof, old_plot_fitted_profiles, partition_bulk_dataset, plot_cluster_profiles, plot_infer_profiles, plot_predicted_expr, pool_bs_seq_rep, predict_expr, preprocess_bs_seq, preprocess_final_HTS_data, process_haib_caltech_wrap, read_anno, read_bs_encode_haib, read_chrom_size, read_expr, read_met, read_rna_encode_caltech, sum_weighted_betareg_grad, sum_weighted_betareg_lik, sum_weighted_bpr_grad, sum_weighted_bpr_lik Package: BRAIN Exports: getAtomsFromSeq, useBRAIN, useBRAIN2, calculateIsotopicProbabilities, calculateAverageMass, calculateMonoisotopicMass, calculateNrPeaks Package: brainflowprobes Exports: brainflowprobes_cov, check_pdf, four_panels, get_nearest_annotation, get_region_cov, plot_coverage, region_info Package: BrainStars Exports: getBrainStars, getBrainStarsFigure Package: branchpointer Exports: gtfToExons, makeBranchpointWindowForExons, makeBranchpointWindowForSNP, plotBranchpointWindow, predictBranchpoints, predictionsToSummary, readQueryFile Package: breakpointR Exports: GenotypeBreaks, breakSeekr, breakpointr, breakpointr2UCSC, deltaWCalculator, exportRegions, hotspotter, loadFromFiles, plotBreakpoints, plotBreakpointsPerChr, plotHeatmap, ranges2UCSC, readBamFileAsGRanges, runBreakpointr, summarizeBreaks, synchronizeReadDir Package: brendaDb Exports: BiocycPathwayEnzymes, BiocycPathwayGenes, DownloadBrenda, ExtractField, ID2Enzyme, QueryBrenda, ReadBrenda, ShowFields, is.brenda.deprecated.entry, is.brenda.entry Package: bridge Exports: bridge.2samples, bridge.3samples Package: BridgeDbR Exports: getSystemCode, getOrganismCode, getBridgeNames, getDatabase, getMatchingSources, getFullName, getDataSource, getAttributes, registerDataSource, loadDatabase, map, fullNameExists, systemCodeExists Package: BrowserViz Exports: BrowserViz, addRMessageHandler, fromJSON, handleResponse, toJSON, webBrowserAvailableForTesting ExportMethods: wait, show, setBrowserWindowTitle, send, roundTripTest, ready, port, getBrowserWindowTitle, getBrowserWindowSize, getBrowserResponse, getBrowserInfo, displayHTMLInDiv, closeWebSocket, browserResponseReady ExportClasses: BrowserViz Package: BSgenome Exports: as.data.frame.BSgenomeViews, saveAsOnDiskLongTable_old, saveRowidsForOnDiskLongTable_old, OnDiskLongTable_old, getBatchesFromOnDiskLongTable_old, getRowsByIndexFromOnDiskLongTable_old, getRowsByIdFromOnDiskLongTable_old, OnDiskLongTable, writeOnDiskLongTable, writeOnDiskLongTableRowids, getBatchesFromOnDiskLongTable, getBatchesBySeqnameFromOnDiskLongTable, getBatchesByOverlapsFromOnDiskLongTable, getRowsFromOnDiskLongTable, getRowsByIdFromOnDiskLongTable, newSNPlocs, newXtraSNPlocs, BSgenome, MaskedBSgenome, installed.genomes, available.genomes, getBSgenome, installed.SNPs, available.SNPs, bsapply, BSgenomeViews, writeBSgenomeToFasta, writeBSgenomeToTwobit, forgeSeqlengthsFile, forgeSeqFiles, forgeMasksFiles, breakpoints, blocksizes, rowids, batchsizes, spatialIndex, referenceGenome, compatibleGenomes, snpcount, snplocs, snpsBySeqname, snpsByOverlaps, snpsById, snpid2loc, snpid2alleles, snpid2grange, SNPlocs_pkgname, sourceUrl, mseqnames, masknames, injectSNPs, forgeBSgenomeDataPkg, forgeMaskedBSgenomeDataPkg ExportMethods: breakpoints, blocksizes, rowids, batchsizes, spatialIndex, referenceGenome, compatibleGenomes, snpcount, snplocs, snpsBySeqname, snpsByOverlaps, snpsById, snpid2loc, snpid2alleles, snpid2grange, SNPlocs_pkgname, sourceUrl, mseqnames, masknames, injectSNPs, forgeBSgenomeDataPkg, forgeMaskedBSgenomeDataPkg, length, names, dim, dimnames, as.character, as.list, as.data.frame, [[, $, unlist, nchar, coerce, show, start, end, width, strand, organism, elementNROWS, ranges, Views, subject, score, seqinfo, seqinfo<-, seqnames, seqnames<-, commonName, provider, providerVersion, releaseDate, releaseName, granges, getSeq, seqtype, alphabetFrequency, hasOnlyBaseLetters, uniqueLetters, letterFrequency, oligonucleotideFrequency, nucleotideFrequencyAt, consensusMatrix, consensusString, matchPWM, countPWM, vmatchPattern, vcountPattern, export ExportClasses: OnDiskLongTable_old, GRanges_OR_NULL, OnDiskLongTable, SNPlocs, ODLT_SNPlocs, OldFashionSNPlocs, InjectSNPsHandler, XtraSNPlocs, BSgenome, MaskedBSgenome, BSgenomeViews, BSgenomeDataPkgSeed Package: bsseq Exports: BSseq, getMeth, getCoverage, getBSseq, getStats, collapseBSseq, orderBSseq, hasBeenSmoothed, chrSelectBSseq, BSmooth, BSmooth.tstat, dmrFinder, fisherTests, combineList, strandCollapse, plotRegion, plotManyRegions, read.umtab, read.umtab2, read.bsmooth, read.bismark, poissonGoodnessOfFit, binomialGoodnessOfFit, data.frame2GRanges, BSseqTstat, BSseqStat, findLoci ExportMethods: assays, assayNames, [, show, seqnames, seqnames<-, seqlevels, seqlevels<-, seqlengths, seqlengths<-, start, start<-, end, end<-, width, width<-, strand, strand<-, granges, dim, nrow, ncol, sampleNames, sampleNames<-, pData, pData<-, findOverlaps, subsetByOverlaps, combine, updateObject ExportClasses: hasGRanges, BSseq, BSseqTstat, BSseqStat, matrixOrNULL Package: BubbleTree Exports: BTreePlotter, trackBTree, BTreePlotter, drawBTree, BTreePlotter, drawBubbles, BTreePlotter, drawFeatures, BTreePredictor, loadRBD, BTreePredictor, btpredict, BTreePredictor, info, Annotate, annoByGenesAndCyto, TrackPlotter, xyTrack, TrackPlotter, bafTrack, TrackPlotter, heteroLociTrack, TrackPlotter, RscoreTrack, TrackPlotter, getTracks, RBD, makeRBD, saveXLS, btcompare 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, [, 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: BUMHMM Exports: nuclPerm, selectNuclPos, scaleDOR, computeStretches, stabiliseVariance, findPatternPos, computeProbs Package: bumphunter Exports: bumphunter, bumphunterEngine, clusterMaker, boundedClusterMaker, dummyData, getSegments, regionFinder, annotateNearest, annotateTranscripts, matchGenes, loessByCluster, runmedByCluster, smoother, locfitByCluster ExportMethods: bumphunter Package: BUS Exports: BUS, pred.network, gene.similarity, gene.trait.similarity, gene.pvalue, gene.trait.pvalue Package: BUScorrect Exports: adjusted_values, baseline_expression_values, BIC_BUS, BUSgibbs, calculate_EPSR_gamma, calculate_EPSR_mu, calculate_EPSR_sigma_sq, estimate_IG_indicators, scale_batch_effects, location_batch_effects, postprob_DE, postprob_DE_thr_fun, subtype_effects, Subtypes, IG_index, visualize_data Package: BUSpaRse Exports: EC2gene, get_velocity_files, make_sparse_matrix, read_count_output, read_velocity_output, save_tr2g_bustools, sort_tr2g, species2dataset, tr2g_EnsDb, tr2g_TxDb, tr2g_ensembl, tr2g_fasta, tr2g_gff3, tr2g_gtf, transcript2gene ExportMethods: get_velocity_files Package: CAFE Exports: ProcessCels, chromosomeStats, bandStats, armStats, fisher.method, cliSubset, discontPlot, discontSmooth, facetPlot, guiSubset, rawPlot, slidPlot, slidSmooth Package: CAGEfightR Exports: assignGeneID, assignMissingID, assignTxID, assignTxType, balanceBC, balanceD, bwCommonGenome, bwGenomeCompatibility, bwValid, calcBidirectionality, calcComposition, calcPooled, calcShape, calcSupport, calcTPM, calcTotalTags, checkPeaked, checkPooled, clusterBidirectionally, clusterUnidirectionally, combineClusters, findLinks, findStretches, quantifyCTSSs, quantifyClusters, quantifyGenes, quickEnhancers, quickTSSs, shapeEntropy, shapeIQR, subsetByBidirectionality, subsetByComposition, subsetBySupport, swapRanges, swapScores, trackBalance, trackCTSS, trackClusters, trackLinks, trimToPeak, trimToPercentiles, tuneTagClustering ExportMethods: trackClusters, trackCTSS, trackBalance, subsetByBidirectionality, combineClusters, calcBidirectionality Package: CAGEr Exports: CTSScoordinatesGR<-, CTSStagCountSE<-, consensusClusters<-, consensusClustersGR<-, consensusClustersSE<-, genomeName<-, inputFiles<-, inputFilesType<-, sampleLabels<-, CAGEexp, CCdataframe2granges, CCgranges2dataframe, CTSSclusteringMethod, CTSScoordinates, CTSScoordinatesGR, CTSScumulativesTagClusters, CTSSnormalizedTpm, CTSSnormalizedTpmDF, CTSSnormalizedTpmDf, CTSSnormalizedTpmGR, CTSStagCount, CTSStagCountDA, CTSStagCountDF, CTSStagCountDf, CTSStagCountGR, CTSStagCountSE, CTSStagCountTable, CTSStoGenes, CustomConsensusClusters, GeneExpDESeq2, GeneExpSE, aggregateTagClusters, annotateCTSS, annotateConsensusClusters, clusterCTSS, consensusClusters, consensusClustersDESeq2, consensusClustersGR, consensusClustersSE, consensusClustersTpm, cumulativeCTSSdistribution, exportCTSStoBedGraph, exportToBed, expressionClasses, extractExpressionClass, findStrandInvaders, genomeName, getCTSS, getExpressionProfiles, getShiftingPromoters, hanabi, hanabiPlot, importPublicData, inputFiles, inputFilesType, librarySizes, mergeCAGEsets, mergeSamples, normalizeTagCount, plotAnnot, plotCorrelation, plotCorrelation2, plotExpressionProfiles, plotInterquantileWidth, plotReverseCumulatives, quantilePositions, removeStrandInvaders, sampleLabels, sampleList, scoreShift, seqNameTotalsSE, setColors, summariseChrExpr, tagClusters, tagClustersGR ExportMethods: show, removeStrandInvaders, findStrandInvaders, coerce ExportClasses: CTSS, CAGEset, CAGEr, CAGEexp Package: calm Exports: CLfdr, EstFDR, EstNullProp_RB Package: CAMERA Exports: annotate, annotateDiffreport, cleanParallel, combinexsAnnos, getIsotopeCluster, getpspectra, findKendrickMasses, findNeutralLoss, findNeutralLossSpecs, pspec2metfrag, pspec2metfusion, xsAnnotate, compoundQuantiles, compoundLibraries, massWindowSizes ExportMethods: setDefaultLists, readLists, setDefaultParams, setParams, generateRules, calcCiS, calcCaS, calcIsotopes, calcPC, calcPC.lpc, calcPC.hcs, getAllPeakEICs, getReducedPeaklist, getPeaklist, plotPsSpectrum, plotEICs, show, findAdducts, groupDen, groupCorr, getAtomCount, getIsotopeProportion, findIsotopes, findIsotopesWithValidation, groupFWHM ExportClasses: ruleSet, compoundQuantiles, xsAnnotate Package: CAMTHC Exports: AfromMarkers, Amat, CAM, CAMASest, CAMMGCluster, CAMPrep, MDL, MGsforA, MGstatistic, PCAmat, Smat, XWProj, cornerSort, redoASest, reselectMG, sffsHull, simplexplot ExportMethods: plot, PCAmat Package: cancerclass Exports: validate, nvalidate, fit, loo, .First.lib, .initFoo, get.d, get.d2, ilogit, calc.roc, calc.auc, get.ntrain, prepare, filter, get.lm ExportMethods: plot3d, summary, plot, predict ExportClasses: validation, nvalidation, predictor, prediction Package: CancerInSilico Exports: calibratePathway, cellSummary, checkDataSet, getAxisAngle, getAxisLength, getCellDistance, getCellPhase, getCellType, getCoordinates, getCycleLength, getDensity, getLocalDensity, getNumberOfCells, getRadius, getTrialAcceptRate, inSilicoCellModel, inSilicoGeneExpression, interactivePlot, plotCells, run ExportClasses: Pathway, OffLatticeModel, GeneExpressionParams, Drug, DrasdoHohmeModel, CellType, CellModel Package: CancerMutationAnalysis Exports: cma.scores, cma.fdr, cma.set.stat, cma.set.sim, extract.sims.method, combine.sims ExportMethods: show ExportClasses: SetMethodsSims Package: CancerSubtypes Exports: DiffExp.limma, ExecuteCC, ExecuteCNMF, ExecuteSNF, ExecuteSNF.CC, ExecuteWSNF, ExecuteiCluster, FSbyCox, FSbyMAD, FSbyPCA, FSbyVar, data.checkDistribution, data.imputation, data.normalization, drawHeatmap, saveFigure, sigclustTest, silhouette_SimilarityMatrix, spectralAlg, survAnalysis Package: CAnD Exports: CAnD, barPlotAncest, calc_combP, getDiffMatrices, plotPvals ExportMethods: test, pValues, overallStatistic, overallpValue, BonfCorr ExportClasses: CAnDResult Package: caOmicsV Exports: bioMatrixLegend, bioNetCircosPlot, bioNetLegend, CA_OMICS_ENV, CA_OMICS_NA_STRING, CA_OMICS_NAME, convertToZScores, drawBioNetNodeBackground, eraseBioNetNode, getBezierCurve, getBioMatrixBasePositions, getBioMatrixColumnPadding, getBioMatrixDataAreaWidth, getBioMatrixDataRowTop, getBioMatrixGeneLabelWidth, getBioMatrixGeneNumber, getBioMatrixLegendHeight, getBioMatrixPhenotypeNumber, getBioMatrixPlotAreaHeigth, getBioMatrixPlotAreaWidth, getBioMatrixRemarkWidth, getBioMatrixRowPadding, getBioMatrixSampleHeight, getBioMatrixSampleIDHeight, getBioMatrixSampleNumber, getBioMatrixSampleWidth, getBioNetBasePositions, getBioNetGraph, getBioNetNodeLinkLine, getBioNetNodePaddingScale, getBioNetNodeParameters, getBioNetNodePlotAreaBoundary, getBioNetNodeRadius, getBioNetPlotAreaWidth, getBioNetPlotLocations, getBioNetPlotSampleWidth, getBioNetPlotTotalSample, getBioNetSamplePlotPosition, getCaOmicsVColors, getCaOmicsVPlotTypes, getDefaultNaStrings, getPlotDataSet, getHeatmapColorScales, getPlotOmicsData, getPlotSampleData, getPlotSummaryData, getRelatedPlotData, initializeBioMatrixPlot, initializeBioNetCircos, labelBioNetNodeNames, linkBioNetNodes, linkBioNetSamples, plotBioMatrix, plotBioMatrixBars, plotBioMatrixBinaryData, plotBioMatrixCategoryData, plotBioMatrixHeatmap, plotBioMatrixRowNames, plotBioMatrixSampleData, plotBioMatrixSampleNames, plotBioNetBars, plotBioNetCircos, plotBioNetHeatmap, plotBioNetLines, plotBioNetPoints, plotBioNetPolygons, plotHeatmapColorScale, setBioMatrixPlotArea, setBioNetNodeLayout, setBioNetPlotAreaBackground, setCaOmicsVColors, setDefaultNaStrings, showBioMatrixPlotLayout, showBioNetNodesLayout, showSupportedBioNetCircosPlotType, sortClinicalData, sortOmicsDataByColumn, sortOmicsDataByRow Package: Cardinal Exports: Binmat, ImageData, IAnnotatedDataFrame, Hashmat, MSImageData, MSImageSet, SImageData, SImageSet, AnnotatedImage, AnnotatedImageList, AnnotatedImagingExperiment, XDataFrame, SummaryDataFrame, PositionDataFrame, MassDataFrame, ImageList, ImageArrayList, MSContinuousImagingSpectraList, MSProcessedImagingSpectraList, SparseImagingExperiment, MSImagingExperiment, addShape, alpha.colors, bw.colors, col.map, color.map, darkmode, discrete.colors, divergent.colors, generateImage, generateSpectrum, gradient.colors, intensity.colors, jet.colors, lightmode, risk.colors, readAnalyze, readImzML, readMSIData, presetImageDef, setup.layout, simulateImage, simulateSpectrum, writeAnalyze, writeImzML, writeMSIData, makeFactor, Cardinal.version, Cardinal.history, mutate, filter, select, summarize, summarise, arrange, group_by, ungroup, slice, groups, collect, viridis, cividis, magma, inferno, plasma, cividis, %>% ExportMethods: topFeatures, topLabels, PCA, PLS, OPLS, spatialFastmap, spatialKMeans, spatialShrunkenCentroids, spatialDGMM, meansTest, segmentationTest, colocalized, coregister, selectROI, batchProcess, process, normalize, smooth, smoothSignal, reduceBaseline, mzAlign, mzBin, mzFilter, peakPick, peakAlign, peakBin, peakFilter, reduceDimension, standardizeRuns, findNeighbors, spatialWeights, crossValidate, cvApply, featureApply, pixelApply, spatialApply, baselineReduction, baselineReduction<-, centroided, centroided<-, normalization, normalization<-, peakPicking, peakPicking<-, smoothing, smoothing<-, spectrumRepresentation, spectrumRepresentation<-, abstract, samples, preproc, preproc<-, pubMedIds, pubMedIds<-, otherInfo, expinfo, notes, notes<-, embeddingMethod, imageShape, instrumentModel, instrumentVendor, inSituChemistry, ionizationType, lineScanDirection, massAnalyzerType, matrixApplication, msiInfo, pixelSize, scanDirection, scanPattern, scanPolarity, scanType, softwareName, softwareVersion, specimenOrigin, specimenType, stainingMethod, tissueThickness, tissueWash, $, $<-, [, [<-, [[, [[<-, annotatedDataFrameFrom, combine, combiner, combiner<-, coord, coord<-, coordinates, coordinates<-, coordnames, coordnames<-, coordLabels, coordLabels<-, dim, dim<-, dims, dimnames, dimnames<-, experimentData, experimentData<-, features, fData, fData<-, featureData, featureData<-, featureNames, featureNames<-, fvarLabels, fvarLabels<-, fvarMetadata, fvarMetadata<-, gridded, gridded<-, height, height<-, iData, iData<-, imageData, imageData<-, intensityData, intensityData<-, initialize, isCentroided, is3D, keys, keys<-, modelData, modelData<-, mz, mz<-, mzData, mzData<-, pData, pData<-, peaks, peaks<-, peakData, peakData<-, phenoData, phenoData<-, pixels, pixelData, pixelData<-, pixelNames, pixelNames<-, positionArray, positionArray<-, processingData, processingData<-, protocolData, protocolData<-, regeneratePositions, resultData, resultData<-, resultNames, resultNames<-, resolution, resolution<-, run, run<-, runNames, runNames<-, sampleNames, sampleNames<-, show, showNames, spectra, spectra<-, storageMode, storageMode<-, tolerance, tolerance<-, varLabels, varLabels<-, varMetadata, varMetadata<-, width, width<-, logLik, fitted, predict, residuals, coef, image, image3D, plot, as.array, as.matrix, as.data.frame, length, names, names<-, rownames, rownames<-, colnames, colnames<-, cbind, rbind, summary ExportClasses: AnnotatedImage, AnnotatedImageList, AnnotatedImagingExperiment, XDataFrame, SummaryDataFrame, PositionDataFrame, MassDataFrame, ImageList, ImageArrayList, SimpleImageList, SimpleImageArrayList, MSContinuousImagingSpectraList, MSProcessedImagingSpectraList, ImagingExperiment, SparseImagingExperiment, MSImagingExperiment, MSContinuousImagingExperiment, MSProcessedImagingExperiment, MSImagingInfo, Binmat, Hashmat, IAnnotatedDataFrame, ImageData, MIAPE-Imaging, MSImageData, MSImageProcess, MSImageSet, ResultSet, SImageData, SImageSet, iSet Package: casper Exports: asymmetryCheck, calcDenovo, calcExp, casperDesign, createDenovoGenome, denovoExpr, getDistrs, getIsland, genePlot, getRoc, matchTranscripts, mergeBatches, mergeExp, modelPrior, pathCounts, plotPriorAS, posprob, probNonEquiv, procBam, procGenome, pvalTreat, qqgammaGenomeWide, qqnormGenomeWide, quantileNorm, relexprByGene, rmShortInserts, simMAE, simMultSamples, simReads, transcripts, variants, variants<-, getReads, getNreads, getChr, getIsland, subsetGenome, txLength, wrapKnown, wrapDenovo, simMAEcheck ExportMethods: plot, lines, coef, [, [[, as.list ExportClasses: annotatedGenome, simulatedSamples, pathCounts, procBam Package: CATALYST Exports: adaptSpillmat, applyCutoffs, assignPrelim, bc_ids, bc_key, cluster, cluster_codes, cluster_ids, compCytof, computeSpillmat, concatFCS, counts, deltas, ei, estCutoffs, extractClusters, filterSCE, guessPanel, launchGUI, marker_classes, mergeClusters, mhl_cutoff, mhl_dists, n_cells, normCytof, normed_bcs, outFCS, outFrames, plotAbundances, plotClusterExprs, plotClusterHeatmap, plotCodes, plotCounts, plotDR, plotDiffHeatmap, plotEvents, plotExprHeatmap, plotExprs, plotMDS, plotMahal, plotMedExprs, plotNRS, plotSpillmat, plotYields, prepData, runDR, sample_ids, sep_cutoffs, state_markers, type_markers, yields ExportMethods: outFrames, outFCS, exprs, sep_cutoffs<-, mhl_cutoff<- ExportClasses: dbFrame, daFrame Package: Category Exports: .doHyperGTest, applyByCategory, cateGOry, cb_children, cb_contingency, cb_parse_band_Hs, cb_parse_band_Mm, cb_sigBands, cb_test, ChrBandTreeFromGraph, DatPkgFactory, exampleLevels, findAMstats, geneIds, geneIds<-, getPathNames, gseattperm, hyperg, makeChrBandGraph, makeChrBandInciMat, makeChrBandGSC, makeEBcontr, NewChrBandTree, MAPAmat, ontology, probes2MAP, probes2Path, ttperm, OBOCollectionDatPkg, OBOHyperGParams, GSEAGOHyperGParams, GSEAKEGGHyperGParams ExportMethods: hyperGTest, linearMTest, universeBuilder, categoryToEntrezBuilder, categoryName, makeValidParams, organism, chrGraph, pvalues, effectSize, geneCounts, universeCounts, universeMappedCount, geneMappedCount, annotation, annotation<-, DatPkgFactory, geneIds, geneIds<-, geneIdsByCategory, geneIdUniverse, testName, pvalueCutoff, pvalueCutoff<-, testDirection, testDirection<-, description, universeGeneIds, ontology, ontology<-, conditional, conditional<-, oddsRatios, expectedCounts, htmlReport, sigCategories, ID2GO, ID2EntrezID, GO2AllProbes, ID2KEGG, KEGG2AllProbes, initialize, show, summary, allGeneIds, childrenOf, level2nodes, lgeneIds, parentOf, treeLevels ExportClasses: DatPkg, AffyDatPkg, YeastDatPkg, Org.XX.egDatPkg, OBOCollectionDatPkg, HyperGParams, GOHyperGParams, KEGGHyperGParams, PFAMHyperGParams, ChrMapHyperGParams, HyperGResultBase, HyperGResult, ChrMapHyperGResult, ChrBandTree, KEGGHyperGResult, PFAMHyperGResult, LinearMParams, ChrMapLinearMParams, LinearMResultBase, LinearMResult, ChrMapLinearMResult Package: categoryCompare ExportMethods: fdr, fdr<-, hyperGTestCC, fdrvalues, listNames, compareNames, compareNames<-, compareIndx, compareColors, compareColors<-, ccType, ccType<-, pvalueType, pvalueType<-, outType, outType<-, minCount, minCount<-, ccEnrich, ccCompare, mainGraph, mainTable, allAnnotation, ccOutCyt, annotation, ontology, geneAnnMapping, graphType, graphType<-, sigID, mergeLists, cwReload, cytOutNodes, cytOutData, resetColors, breakEdges, pvalueCutoff, pvalueCutoff<- ExportClasses: HyperGParamsCC, GOHyperGParamsCC, KEGGHyperGParamsCC, HyperGResultCC, GOHyperGResultCC, KEGGHyperGResultCC, ccOptions, ccGeneList, ccEnrichResult, GOccEnrichResult, KEGGccEnrichResult, ccEnrichCollection, ccCompareResult, ccCompareCollection, ccSigList, GENccEnrichResult, mergedData Package: CausalR Exports: AnalysePredictionsList, CalculateEnrichmentPValue, CalculateSignificance, CalculateSignificanceUsingCubicAlgorithm, CalculateSignificanceUsingCubicAlgorithm1b, CalculateSignificanceUsingQuarticAlgorithm, CompareHypothesis, CreateCCG, CreateCG, GetNodeName, GetNumberOfPositiveAndNegativeEntries, GetShortestPathsFromCCG, MakePredictions, MakePredictionsFromCCG, MakePredictionsFromCG, PlotGraphWithNodeNames, RankTheHypotheses, ReadExperimentalData, ScoreHypothesis, WriteAllExplainedNodesToSifFile, WriteExplainedNodesToSifFile, runSCANR Package: cbaf Exports: automatedStatistics, availableData, cleanDatabase, heatmapOutput, obtainMultipleStudies, obtainOneStudy, processMultipleStudies, processOneStudy, xlsxOutput Package: ccfindR Exports: basis<-, coeff<-, dbasis<-, measure<-, ranks<-, assignCelltype, basis, build_tree, cell_map, cluster_id, coeff, dbasis, dcoeff, factorize, feature_map, filter_cells, filter_genes, gene_map, measure, meta_gene.cv, meta_genes, newick, normalize_count, optimal_rank, plot_genes, plot_tree, ranks, read_10x, remove_zeros, rename_tips, scNMFSet, simulate_data, simulate_whx, vb_factorize, visualize_clusters, write_10x, write_meta ExportMethods: show, rowData, plot, counts, colData, rowData<-, ranks<-, measure<-, counts<-, colData<-, coeff<-, basis<- Package: ccmap Exports: get_dprimes, query_combos, query_drugs, sum_rowcolCumsum Package: CCPROMISE Exports: CCPROMISE, PrbPROMISE, CANN, PROMISE2, PrbCor Package: ccrepe Exports: ccrepe, nc.score Package: celaref Exports: contrast_each_group_to_the_rest, contrast_each_group_to_the_rest_for_norm_ma_with_limma, convert_se_gene_ids, get_rankstat_table, get_the_up_genes_for_all_possible_groups, get_the_up_genes_for_group, load_dataset_10Xdata, load_se_from_files, load_se_from_tables, make_ranking_violin_plot, make_ref_similarity_names, make_ref_similarity_names_using_marked, subset_cells_by_group, trim_small_groups_and_low_expression_genes Package: celda Exports: appendCeldaList, availableModels, bestLogLikelihood, celda, celdaGridSearch, celdaHeatmap, celdaPerplexity, celdaProbabilityMap, celdaTsne, celdaUmap, celda_C, celda_CG, celda_G, clusterProbability, clusters, compareCountMatrix, countChecksum, decontX, differentialExpression, distinctColors, factorizeMatrix, featureModuleLookup, featureModuleTable, findMarkers, geneSetEnrich, getDecisions, logLikelihood, logLikelihoodHistory, logLikelihoodcelda_C, logLikelihoodcelda_CG, logLikelihoodcelda_G, matrixNames, moduleHeatmap, normalizeCounts, params, perplexity, plotDendro, plotDimReduceCluster, plotDimReduceFeature, plotDimReduceGrid, plotDimReduceModule, plotGridSearchPerplexity, plotGridSearchPerplexitycelda_C, plotGridSearchPerplexitycelda_CG, plotGridSearchPerplexitycelda_G, plotHeatmap, recodeClusterY, recodeClusterZ, recursiveSplitCell, recursiveSplitModule, resList, resamplePerplexity, runParams, sampleLabel, selectBestModel, simulateCells, simulateCellscelda_C, simulateCellscelda_CG, simulateCellscelda_G, simulateContaminatedMatrix, subsetCeldaList, topRank, violinPlot ExportMethods: sampleLabel, runParams, resList, perplexity, params, matrixNames, logLikelihoodHistory, featureModuleLookup, factorizeMatrix, countChecksum, clusters, clusterProbability, celdaUmap, celdaTsne, celdaProbabilityMap, celdaPerplexity, celdaHeatmap, bestLogLikelihood Package: cellbaseR Exports: CellBaseParam, CellBaseR, createGeneModel, getCaddScores, getCellBaseResourceHelp, getClinicalByGene, getClinicalByRegion, getConservationByRegion, getGeneInfo, getProteinInfo, getRegulatoryByRegion, getSnpByGene, getTfbsByRegion, getTranscriptByGene, getVariantAnnotation ExportMethods: getXref, getVariant, getTranscript, getTf, getSnp, getRegion, getProtein, getMeta, getGene, getClinical, getChromosomeInfo, getCellBase, AnnotateVcf ExportClasses: CellBaseR, CellBaseParam Package: CellBench Exports: all_unique, any_task_errors, apply_methods, apply_metrics, arrow_sep, as_pipeline_list, begin_benchmark, cache_method, cellbench_case_study, cellbench_file, clear_cached_datasets, clear_cellbench_cache, data_list, filter_zero_genes, fn_arg_seq, fn_list, is.task_error, is_all_of, is_one_of, keep_high_count_cells, keep_high_count_genes, keep_high_var_genes, load_all_data, load_cell_mix_data, load_mrna_mix_data, load_sc_data, mhead, pipeline_collapse, sample_cells, sample_genes, set_cellbench_bpparam, set_cellbench_cache_path, set_cellbench_threads, strip_timing, time_methods, unpack_timing Package: cellHTS2 Exports: oneRowPerId, Bscore, buildCellHTS2, configurationAsScreenPlot, convertOldCellHTS, convertWellCoordinates, getEnVisionRawData, getEnVisionCrosstalkCorrectedData, getDynamicRange, getMeasureRepAgreement, getTopTable, getSettings, getZfactor, gseaModule, imageScreen, normalizePlates, plotSpatialEffects, readPlateList, readHTAnalystData, rsa, scores2calls, scoreReplicates, setSettings, spatialNormalization, summarizeChannels, summarizeReplicates, templateDescriptionFile, updateCellHTS, writeReport, write.tabdel ExportMethods: annotate, batch, batch<-, compare2cellHTS, coerce, configure, Data, Data<-, geneAnno, initialize, intensityFiles, lines, meanSdPlot, name, name<-, nbatch, pdim, plate, plateConf, plateEffects, plateList, plot, position, ROC, screenDesc, screenLog, show, state, well, wellAnno, writeTab ExportClasses: cellHTS, ROC Package: cellity Exports: assess_cell_quality_PCA, assess_cell_quality_SVM, extract_features, normalise_by_factor Package: CellMapper Exports: CMprep, CMsearch, CellMapperList, ReplicateManuscript ExportMethods: show ExportClasses: CellMapperList Package: CellMixS Exports: cms, entropy, evalIntegration, isi, ldfDiff, ldfSce, locStructure, mixMetric, visCluster, visGroup, visHist, visIntegration, visMetric, visOverview Package: CellNOptR Exports: buildBitString, checkSignals, exhaustive, CNOdata, CNORwrap, CNORbool, CNOlist, compressModel, computeScoreT1, computeScoreTN, crossInhibitedData, cSimulator, cutAndPlot, cutAndPlotResultsT1, cutAndPlotResultsTN, cutCNOlist, cutNONC, cutSimList, cutModel, defaultParameters, expandGates, findNONC, gaBinaryT1, gaBinaryT2, gaBinaryTN, graph2sif, getFit, indexFinder, mapBack, makeCNOlist, model2sif, model2igraph, normaliseCNOlist, plotCNOlist, plotCNOlist2, plotCNOlistLarge, plotCNOlistLargePDF, plotCNOlistPDF, plotFit, plotOptimResults, plotOptimResultsPan, plotOptimResultsPDF, prep4sim, prep4Sim, preprocessing, randomizeCNOlist, readSBMLQual, readMIDAS, readSIF, readSif, readBND, readBNET, residualError, sif2graph, simulateT1, simulateTN, simulatorT0, simulatorT1, simulatorTN, toSBML, writeDot, writeMIDAS, writeSIF, writeNetwork, writeReport, writeScaffold, plotModel ExportMethods: setSignals<-, getCues, getSignals, getStimuli, getInhibitors, getVariances, getTimepoints, plot, randomize, length, compatCNOlist, readErrors, writeErrors ExportClasses: CNOlist Package: cellscape Exports: cellscape, cellscapeOutput, checkAlpha, checkClonalPrev, checkCloneColours, checkGtypePositioning, checkMinDims, checkPerts, checkRequiredInputs, checkTreeEdges, dfs_tree, findMode, getMutationsData, renderCnvTree, replaceSpaces Package: CellScore Exports: BarplotOnOff, BoxplotCellScore, CellScore, CellScoreReport, CosineSimScore, OnOff, PcaStandards, PlotCosineSimHeatmap, RugplotCellScore, ScatterplotCellScoreComponents, extractTransitions, heatmapOnOffMarkers, rugplotDonorTargetTest, scatterplotDonorTargetTest Package: CellTrails Exports: latentSpace<-, manifold2D<-, stateTrajLayout<-, states<-, trailNames<-, trajFeatureNames<-, trajLayout<-, userLandmarks<-, addTrail, connectStates, contrastTrailExpr, embedSamples, enrichment.test, filterTrajFeaturesByCOV, filterTrajFeaturesByDL, filterTrajFeaturesByFF, findSpectrum, findStates, fitDynamic, fitTrajectory, landmarks, latentSpace, manifold2D, pca, phenoNames, plotDynamic, plotManifold, plotMap, plotStateExpression, plotStateSize, plotStateTrajectory, plotTrail, plotTrajectoryFit, read.ygraphml, removeTrail, selectTrajectory, showTrajInfo, simulate_exprs, states, trailNames, trails, trajComponents, trajFeatureNames, trajLayout, trajResiduals, trajSampleNames, userLandmarks, write.ygraphml ExportMethods: sampleNames, featureNames Package: cellTree Exports: cell.ordering.table, compute.backbone.tree, compute.go.enrichment, compute.lda, ct.plot.go.dag, ct.plot.grouping, ct.plot.heatmap, ct.plot.topics, get.cell.dists, go.results.to.latex Package: CEMiTool Exports: adj_data<-, expr_data<-, interactions_data<-, mod_colors<-, sample_annotation<-, adj_data, cem_overlap, cemitool, diagnostic_report, enrich_mods, expr_data, filter_genes, find_modules, fit_data, generate_report, get_adj, get_beta_data, get_cemitool_r2_beta, get_connectivity, get_hubs, get_merged_mods, get_mods, get_phi, gsea_data, interactions_data, mod_colors, mod_gene_num, mod_gsea, mod_names, mod_ora, mod_summary, module_genes, new_cem, nmodules, ora_data, overlap_community, plot_beta_r2, plot_comembership, plot_consensus, plot_gsea, plot_hist, plot_interactions, plot_mean_k, plot_mean_var, plot_ora, plot_profile, plot_qq, plot_sample_tree, plot_similarity, read_gmt, sample_annotation, save_plots, select_genes, show_plot, stat_overlap_mods, write_files ExportMethods: show, interactions_data, get_phi, get_beta_data, find_modules Package: CexoR Exports: cexor, plotcexor Package: CGEN Exports: snp.logistic, getSummary, getWaldTest, QQ.plot, Manhattan.plot, snp.effects, getMatchedSets, snp.matched, printEffects, additive.test, snp.effects.plot, GxE.scan, GxE.scan.combine, GxE.scan.partition, snp.score Package: CGHbase Exports: make_cghRaw ExportMethods: initialize, plot.cghRaw, plot.cghSeg, plot.cghCall, plot.cghRegions, frequencyPlot, chromosomes, bpstart, bpend, avedist, nclone, copynumber, segmented, calls, regions, probloss, probnorm, probgain, probamp ExportClasses: cghRaw, cghSeg, cghCall, cghRegions Package: CGHcall ExportMethods: initialize ExportClasses: cghRaw, cghSeg, cghCall Package: cghMCR Exports: cghMCR, plot.DNAcopy, MCR, mergeMCRProbes, SGOL ExportMethods: gol, plot ExportClasses: cghMCR, SGOL Package: ChAMP Exports: champ.process, champ.load, champ.import, champ.filter, champ.impute, champ.QC, champ.norm, champ.SVD, champ.runCombat, champ.DMP, champ.DMR, champ.Block, champ.GSEA, champ.ebGSEA, champ.EpiMod, champ.CNA, champ.refbase, DMP.GUI, DMR.GUI, QC.GUI, CpG.GUI, Block.GUI Package: CHARGE Exports: bimodalTest, clusterExpr, cvExpr, exprFinder, pcaExpr, plotcvExpr Package: ChemmineOB Exports: convertFormat, convertFormatFile, convertToImage, prop_OB, fingerprint_OB, smartsSearch_OB, exactMass_OB, canonicalNumbering_OB, forEachMol Package: ChemmineR Exports: atomprop, pubchemFPencoding, read.SDFstr, read.SDFset, read.SMIset, sdfStream, read.AP, read.SDFindex, write.SDF, write.SMI, write.SDFsplit, validSDF, makeUnique, atomcountMA, MW, MF, datablock2ma, splitNumChar, grepSDFset, conMA, bonds, groups, rings, atomsubset, SDFset, maximallyDissimilar, plotStruc, openBabelPlot, draw_sdf, SDF2apcmp, sdf2ap, apset2descdb, desc2fp, cmp.search, cmp.similarity, cmp.parse, cmp.parse1, sdf.subset, db.explain, cluster.sizestat, cmp.duplicated, sdf.visualize, db.subset, smiles2sdf, sdf2smiles, propOB, fingerprintOB, regenerateCoords, smartsSearchOB, exactMassOB, generate3DCoords, canonicalize, canonicalNumbering, largestComponent, fp2bit, fpSim, getIds, searchString, searchSim, sdf2smiles, smiles2sdf, pubchemCidToSDF, pubchemSmilesSearch, pubchemSDFSearch, pubchemName2CID, cmp.cluster, jarvisPatrick, cluster.visualize, nearestNeighbors, trimNeighbors, fromNNMatrix, byCluster, initDb, loadSdf, loadSmiles, getCompounds, findCompounds, getCompoundNames, findCompoundsByName, addNewFeatures, listFeatures, jarvisPatrick_c, genAPDescriptors, addDescriptorType, setPriorities, randomPriorities, forestSizePriorities, getAllCompoundIds, getCompoundFeatures, bufferLines, bufferResultSet, parBatchByIndex, batchByIndex, selectInBatches, dbTransaction, DUD, DrugBank, status, browseJob, result, listCMTools, toolDetails, launchCMTool, genParameters, SDFDataTable ExportMethods: sdfstr2list, sdf2list, sdf2str, SDFset2list, SDFset2SDF, sdfstr2list<-, SDFset2SDF<-, cid<-, header<-, atomblock<-, bondblock<-, datablock<-, [, [[, [<-, [[<-, coerce, show, length, c, plot, as.matrix, header, atomblock, bondblock, datablock, view, cid, sdfid, atomcount, datablocktag, obmol, fold, foldCount, fptype, numBits, ap ExportClasses: SDFstr, SDF, SDFset, SMI, SMIset, AP, APset, FP, FPset, jobToken Package: CHETAH Exports: CHETAHclassifier, CHETAHshiny, Classify, ClassifyReference, CorrelateReference, PlotCHETAH, PlotTSNE, PlotTree, RenameBelowNode Package: ChIC Exports: chicWrapper, createMetageneProfile, getCrossCorrelationScores, getPeakCallingScores, listAvailableElements, listDatasets, metagenePlotsForComparison, plotReferenceDistribution, predictionScore, qualityScores_EM, qualityScores_GM, qualityScores_LM, qualityScores_LMgenebody, readBamFile, removeLocalTagAnomalies, tagDensity Package: Chicago Exports: chicagoPipeline, copyCD, defaultSettings, estimateBrownianComponent, estimateBrownianNoise, estimateDistFun, plotDistFun, estimateTechnicalNoise, exportResults, exportToGI, getPvals, getScores, mergeSamples, modifySettings, normaliseBaits, normaliseOtherEnds, plotBaits, readAndMerge, readSample, setExperiment, overlapFragWithFeatures, peakEnrichment4Features, chicagoData, getSkOnly ExportMethods: intData, settings, params, intData<-, params<- Package: chimera Exports: plotCoverage, is.fSet Package: chimeraviz Exports: downstream_partner_gene<-, partner_gene_ensembl_id<-, upstream_partner_gene<-, add_fusion_reads_alignment, create_fusion_report, decide_transcript_category, down_shift, downstream_partner_gene, fetch_reads_from_fastq, fusion_spanning_reads_count, fusion_split_reads_count, fusion_to_data_frame, get_ensembl_ids, get_fusion_by_chromosome, get_fusion_by_gene_name, get_fusion_by_id, get_transcripts_ensembl_db, import_defuse, import_ericscript, import_fusioncatcher, import_fusionmap, import_infusion, import_jaffa, import_oncofuse, import_prada, import_soapfuse, import_starfusion, partner_gene_ensembl_id, partner_gene_junction_sequence, plot_circle, plot_fusion, plot_fusion_reads, plot_fusion_separate, plot_fusion_together, plot_fusion_transcript, plot_fusion_transcript_with_protein_domain, plot_fusion_transcripts_graph, plot_transcripts, select_transcript, split_on_utr_and_add_feature, upstream_partner_gene, write_fusion_reference ExportClasses: PartnerGene, Fusion Package: ChIPanalyser ExportMethods: averageExpPWMScore, backgroundSignal, backgroundSignal<-, boundMolecules, boundMolecules<-, BPFrequency, BPFrequency<-, chipMean, chipMean<-, chipSd, chipSd<-, chipSmooth, chipSmooth<-, DNASequenceLength, drop, initialize, lambdaPWM, lambdaPWM<-, loci, lociWidth, lociWidth<-, maxPWMScore, maxSignal, maxSignal<-, minPWMScore, naturalLog, naturalLog<-, noiseFilter, noiseFilter<-, noOfSites, noOfSites<-, PFMFormat, PFMFormat<-, ploidy, ploidy<-, PositionFrequencyMatrix, PositionFrequencyMatrix<-, PositionWeightMatrix, PositionWeightMatrix<-, profiles, PWMpseudocount, PWMpseudocount<-, PWMThreshold, PWMThreshold<-, removeBackground, removeBackground<-, scores, show, stepSize, stepSize<-, strandRule, strandRule<-, whichstrand, whichstrand<- ExportClasses: loci, genomicProfiles, genomicProfilesInternal, parameterOptions, ChIPScore, GRList, nos Package: ChIPComp Exports: makeConf, ChIPComp, makeCountSet Package: chipenrich Exports: assign_peak_segments, assign_peaks, broadenrich, calc_peak_gene_overlap, chipenrich, hybridenrich, load_peaks, num_peaks_per_gene, peaks2genes, plot_chipenrich_spline, plot_dist_to_tss, plot_gene_coverage, plot_polyenrich_spline, polyenrich, proxReg, read_bed, supported_genesets, supported_genomes, supported_locusdefs, supported_methods, supported_read_lengths Package: ChIPexoQual Exports: ARCvURCplot, ExoData, ExoDataBlacklist, ExoDataSubsampling, FSRDistplot, MAplot, beta1, beta2, calculateParamDist, formatRegions, nreads, paramDist, paramDistBoxplot, regionCompplot ExportMethods: nreads ExportClasses: ExoData Package: ChIPpeakAnno Exports: addAncestors, addGeneIDs, addMetadata, annoPeaks, annotatePeakInBatch, assignChromosomeRegion, binOverFeature, binOverGene, binOverRegions, condenseMatrixByColnames, convert2EntrezID, countPatternInSeqs, cumulativePercentage, egOrgMap, estFragmentLength, estLibSize, featureAlignedExtendSignal, featureAlignedDistribution, featureAlignedHeatmap, featureAlignedSignal, findEnhancers, findOverlappingPeaks, findOverlapsOfPeaks, getAllPeakSequence, getAnnotation, getEnrichedGO, getEnrichedPATH, getUniqueGOidCount, getVennCounts, hyperGtest, IDRfilter, makeVennDiagram, mergePlusMinusPeaks, oligoFrequency, oligoSummary, peakPermTest, peaksNearBDP, plotBinOverRegions, pie1, preparePool, reCenterPeaks, summarizeOverlapsByBins, summarizePatternInPeaks, tileGRanges, tileCount, toGRanges, translatePattern, write2FASTA, xget ExportMethods: $, $<-, info, annoGR ExportClasses: bindist, permPool, annoGR Package: ChIPQC Exports: ChIPQCsample, ChIPQC ExportMethods: averagepeaksignal, coveragehistogram, crosscoverage, flagtagcounts, fragmentlength, FragmentLengthCrossCoverage, Normalisedaveragepeaksignal, peaks, ReadLengthCrossCoverage, RelativeCrossCoverage, show, ssd, readlength, plotCC, plotPeakProfile, plotFrip, plotFribl, plotRap, plotCoverageHist, plotRegi, frip, rip, ribl, regi, mapped, QCmetrics, QCsample, QCcontrol, QCmetadata, QCannotation, QCdba, plotSSD, reads, duplicates, duplicateRate, plotCorHeatmap, plotPrincomp, ChIPQCreport ExportClasses: ChIPQCsample, ChIPQCexperiment Package: ChIPseeker Exports: ., GRangesList, annotatePeak, as.GRanges, covplot, downloadGEObedFiles, downloadGSMbedFiles, dropAnno, enrichAnnoOverlap, enrichPeakOverlap, getBioRegion, getGEOInfo, getGEOgenomeVersion, getGEOspecies, getPromoters, getSampleFiles, getTagMatrix, overlap, peakHeatmap, plotAnnoBar, plotAnnoPie, plotAnnoPie.csAnno, plotAvgProf, plotAvgProf2, plotDistToTSS, readPeakFile, seq2gene, shuffle, tagHeatmap, vennpie, vennplot, vennplot.peakfile ExportMethods: vennpie, upsetplot, show, plotDistToTSS, plotAnnoPie, plotAnnoBar ExportClasses: csAnno Package: chipseq Exports: diffPeakSummary, laneSubsample, chipseqFilter, islandDepthPlot, coverageplot, sparse.density, basesCovered, densityCorr, estimate.mean.fraglen, subsetSummary, peakCutoff, peakSummary ExportMethods: estimate.mean.fraglen Package: ChIPseqR ExportMethods: strandPileup, callBindingSites, [[, [, $, names, [[<-, [<-, $<-, names<-, lapply, sapply, as.data.frame, head, tail, min, max, range, nreads, chrLength, score, pvalue, peaks, cutoff, cutoff<-, nullDist, nullDist<-, plot, compress, decompress ExportClasses: ReadCounts, BindScore, RLEReadCounts, RLEBindScore Package: ChIPSeqSpike Exports: ChIPSeqSpikeDataset, ChIPSeqSpikeDatasetBoost, spikeDataset, spikePipe, Experiment, ExperimentLoaded ExportMethods: plotProfile, plotTransform, plotHeatmaps, boxplotSpike, plotCor, exportBigWigs, estimateScalingFactors, scaling, inputSubtraction, extractBinding, getBam, getBigWigFile, getExperimentListBigWigs, getExpName, getScalingFactor, getExogenousScalingFactor, getCount, getExoCount, getAverageBindingValues, getMatBindingValues, getLoadedData, getExogenousBam, spikeSummary, getRatio, getDatasetList, getExperimentList, scalingFactor<-, exogenousScalingFactor<-, count<-, exoCount<-, bigWigFile<-, averageBindingValues<-, matBindingValues<-, datasetList<-, experimentList<- ExportClasses: ChIPSeqSpikeDataset, ChIPSeqSpikeDatasetBoost, ChIPSeqSpikeDatasetList, ChIPSeqSpikeDatasetListBoost, Experiment, ExperimentLoaded Package: ChIPXpress Exports: ChIPXpress, buildDatabase, cleanDatabase Package: chopsticks Exports: epsout.ld.snp, glm.test.control, ibs.stats, ibsCount, ibsDist, ld.snp, ld.with, niceprint, pair.result.ld.snp, plot.snp.dprime, print.snp.dprime, qq.chisq, read.HapMap.data, read.pedfile.info, read.snps.chiamo, read.snps.long, read.snps.long.old, read.snps.pedfile, read.wtccc.signals, row.summary, single.snp.tests, snp.cbind, snp.rbind, snp.cor, snp.lhs.tests, snp.post, snp.pre, snp.rhs.tests, write.snp.matrix, xxt, convert.snpMatrix, convert.snpMatrix.dir ExportMethods: cbind2, rbind2, is.na, ld.with, show, summary, [, [<-, coerce, initialize ExportClasses: snp.matrix, X.snp.matrix, snp, X.snp, snp.dprime Package: chromDraw Exports: chromDrawGR Package: ChromHeatMap Exports: plotChrMap, makeChrStrandData, grabChrMapProbes, makeRangedDataList, createChrMatrix, chrHeatMap, drawMapDendro ExportMethods: chrNames ExportClasses: ChrStrandData, ChrStrandMatrix, ChrMapPlot Package: chromPlot Exports: chromPlot Package: chromstaR Exports: Chromstar, bin2dec, binReads, callPeaksMultivariate, callPeaksReplicates, callPeaksUnivariate, changeFDR, changeMaxPostCutoff, changePostCutoff, collapseBins, combineMultivariates, dec2bin, exportCombinations, exportCounts, exportGRangesAsBedFile, exportPeaks, fixedWidthBins, genomicFrequencies, getCombinations, getDistinctColors, getStateColors, heatmapCombinations, heatmapCountCorrelation, heatmapTransitionProbs, loadHmmsFromFiles, plotEnrichCountHeatmap, plotEnrichment, plotExpression, plotFoldEnrichHeatmap, plotGenomeBrowser, plotHistogram, readBamFileAsGRanges, readBedFileAsGRanges, readCustomBedFile, removeCondition, stateBrewer, transitionFrequencies, unis2pseudomulti, variableWidthBins Package: chromswitch Exports: GRangesToCoord, NMI, binarizePeaks, callBinary, callSummary, classEntropy, cluster, clusterEntropy, completeness, conditionalClassEntropy, conditionalClusterEntropy, coordToGRanges, filterPeaks, homogeneity, makeBrowserCoord, normalizePeaks, pReciprocalOverlap, purity, readNarrowPeak, reducePeaks, retrievePeaks, summarizePeaks, vMeasure, winsorNorm ExportMethods: samples, region, peaks Package: chromVAR Exports: addGCBias, annotationMatches, assembleKmers, chromVAR_theme, computeDeviations, computeExpectations, computeVariability, deviationsCovariability, deviationsTsne, differentialDeviations, differentialVariability, filterPeaks, filterSamples, filterSamplesPlot, getAnnotationCorrelation, getAnnotationSynergy, getAnnotations, getBackgroundPeaks, getCisGroups, getCounts, getFragmentsPerPeak, getFragmentsPerSample, getJasparMotifs, getPeaks, getPermutedData, getSampleCorrelation, getSampleDepths, getSampleDistance, getTotalFragments, makeBiasBins, makePermutedSets, matchKmers, plotDeviationsTsne, plotKmerMismatch, plotVariability, pwmDistance, readNarrowpeaks ExportMethods: rbind, matchKmers, makePermutedSets, makeBiasBins, getTotalFragments, getFragmentsPerSample, getFragmentsPerPeak, getCisGroups, getBackgroundPeaks, getAnnotations, getAnnotationSynergy, getAnnotationCorrelation, deviations, deviationScores, counts, computeExpectations, computeDeviations, cbind, addGCBias, counts<-, annotationMatches<- Package: CHRONOS Exports: CHRONOSrun, downloadPathways, downloadKEGGPathwayList, downloadMiRecords, createPathwayGraphs, extractLinearSubpathways, extractNonLinearSubpathways, scoreSubpathways, pathwayMeasures, importExpressions, visualizeResults, convertNomenclature, convertMiRNANomenclature, subpathwayKEGGmap, subpathwayMiRNAs, getEdgeTypes Package: cicero Exports: aggregate_by_cell_bin, aggregate_nearby_peaks, annotate_cds_by_site, assemble_connections, build_gene_activity_matrix, compare_connections, df_for_coords, estimate_distance_parameter, find_overlapping_ccans, find_overlapping_coordinates, generate_ccans, generate_cicero_models, make_atac_cds, make_cicero_cds, normalize_gene_activities, plot_accessibility_in_pseudotime, plot_connections, ranges_for_coords, run_cicero Package: CINdex Exports: comp.heatmap, extract.genes.in.cyto.regions, run.cin.chr, run.cin.cyto, ttest.cyto.cin.heatmap Package: circRNAprofiler Exports: annotateBSJs, annotateRepeats, annotateSNPsGWAS, checkProjectFolder, filterCirc, formatGTF, getBackSplicedJunctions, getCircSeqs, getDeseqRes, getDetectionTools, getEdgerRes, getMiRsites, getMotifs, getRandomBSJunctions, getRegexPattern, getSeqsAcrossBSJs, getSeqsFromGRs, importCircExplorer2, importCircMarker, importKnife, importMapSplice, importNCLscan, importOther, importUroborus, initCircRNAprofiler, liftBSJcoords, mergeBSJunctions, mergeMotifs, plotExBetweenBSEs, plotExPosition, plotHostGenes, plotLenBSEs, plotLenIntrons, plotMiR, plotMotifs, plotTotExons, rearrangeMiRres, volcanoPlot Package: cisPath Exports: cisPath, networkView, easyEditor, getMappingFile, formatPINAPPI, formatSIFfile, formatSTRINGPPI, formatiRefIndex, combinePPI Package: cleanUpdTSeq Exports: BED2GRangesSeq, getUpstreamSequence, getDownstreamSequence, buildFeatureVector, predictTestSet, buildClassifier ExportMethods: $, $<- ExportClasses: modelInfo, PASclassifier, featureVector Package: cleaver ExportMethods: cleave, cleavageRanges, cleavageSites Package: clippda Exports: sampleClusteredData, negativeIntensitiesCorrection ExportMethods: show ExportClasses: aclinicalProteomicsData Package: clipper Exports: cliqueVarianceTest, cliqueMeanTest, cliqueMixedTest, getGraphEntryGenes, getJunctionTreePaths, pathQ, clipper, prunePaths, easyClip, plotInCytoscape, nameCliques, deleteEdge, easyLook, clipperAllRoots, cliquePairedTest Package: cliqueMS Exports: computeCliques, createNetwork, createanClique, getAnnotation, getCliques, getIsotopes, getlistofCliques, getIsolistanClique, getNetanClique, getNetanClique<-, getPeaklistanClique, getPeaklistanClique<-, hasAnnotation, hasAnnotation<-, hasCliques, hasCliques<-, hasIsotopes, hasIsotopes<- ExportMethods: show, hasIsotopes<-, hasIsotopes, hasCliques<-, hasCliques, hasAnnotation<-, hasAnnotation, getPeaklistanClique<-, getPeaklistanClique, getNetanClique<-, getNetanClique, getIsolistanClique, getlistofCliques<-, getlistofCliques, createanClique, createNetwork Package: Clomial Exports: Clomial, choose.best, Clomial.generate.data, Clomial.iterate, compute.bic, Clomial.likelihood, compute.errors Package: Clonality Exports: SNVtest2, create.mutation.matrix, get.mutation.frequencies, clonEM, grid.lik, mutation.rem, mutation.proba, SNVtest, ave.adj.probes, chromosomePlots, clonality.analysis, genomewidePlots, histogramPlot, LOHclonality, splitChromosomes, ECMtesting, LRtesting3or4tumors Package: clonotypeR Exports: clonotype_table, common_clonotypes, is_unproductive, private_clonotypes, read_clonotypes, unique_clonotypes, yassai_identifier 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: CluMSID Exports: HCplot, HCtbl, MDSplot, OPTICSplot, OPTICStbl, accessAnnotation, accessID, accessNeutralLosses, accessPolarity, accessPrecursor, accessRT, accessSpectrum, addAnnotations, as.MS2spectrum, cossim, distanceMatrix, extractMS2spectra, extractPseudospectra, featureList, findFragment, findNL, getSimilarities, getSpectrum, mergeMS2spectra, networkplot, specplot, splitPolarities, writeFeaturelist ExportMethods: show, rtime, precursorMz, peaksCount, mz, intensity, cossim ExportClasses: pseudospectrum, MS2spectrum Package: clusterExperiment Exports: ClusterExperiment, ClusterFunction, bigPalette, internalFunctionCheck, listBuiltInFilterStats, listBuiltInFunctions, listBuiltInReducedDims, listBuiltInType01, listBuiltInTypeK, makeBlankData, massivePalette, numericalAsCharacter, seqCluster, seqPal1, seqPal2, seqPal3, seqPal4, seqPal5, setBreaks, showHeatmapPalettes, showPalette ExportMethods: workflowClusters, workflowClusterTable, workflowClusterDetails, updateObject, transformation, transformData, tableClusters, subsetByCluster, subsampleClustering, show, setToFinal, setToCurrent, sampleDendrogram, requiredArgs, renameClusters, removeUnassigned, removeClusters, removeClusterings, recolorClusters, primaryClusterType, primaryClusterNamed, primaryClusterLabel, primaryClusterIndex, primaryCluster, plotReducedDims, plotHeatmap, plotFeatureScatter, plotFeatureBoxplot, plotDendrogram, plotContrastHeatmap, plotCoClustering, plotClustersWorkflow, plotClustersTable, plotClusters, plotClusterLegend, plotBarplot, orderSamples, nodeMergeInfo, nodeLabels, nodeIds, nTips, nSamples, nNodes, nInternalNodes, nFeatures, nClusters, nClusterings, mergeMethod, mergeCutoff, mergeClusters, mergeClusterIndex, makeReducedDims, makeFilterStats, makeDendrogram, makeConsensus, mainClustering, inputType, getSingleClusterIndex, getPostProcessingArgs, getMergeCorrespond, getClusterManyParams, getClusterIndex, getBuiltInFunction, getBestFeatures, filterNames, filterData, eraseMergeInfo, dendroClusterIndex, defaultNDims, convertToDendrogram, convertClusterLegend, combineMany, colDataClusters, coClustering, clusteringInfo, clusterTypes, clusterSingle, clusterMatrixNamed, clusterMatrixColors, clusterMatrix, clusterMany, clusterLegend, clusterLabels, clusterDendrogram, clusterContrasts, checkDendrogram, assignUnassigned, algorithmType, addToColData, addClusterings, RSEC, ClusterFunction, ClusterExperiment, transformation<-, primaryClusterIndex<-, orderSamples<-, nodeLabels<-, coClustering<-, clusterTypes<-, clusterLegend<-, clusterLabels<-, [ ExportClasses: ClusterFunction, ClusterExperiment Package: ClusterJudge Exports: attribute_mut_inf, clusterJudge, clusterJudge_z_score, entities_attribute_stats, consolidate_entity_attribute, validate_association, download_Yeast_Go_terms, convert_Yeast_SGDId_2_systematic, download_Yeast_GO_mapping Package: clusterProfiler Exports: GSEA, Gff2GeneTable, bitr, bitr_kegg, browseKEGG, buildGOmap, cnetplot, compareCluster, dotplot, download_KEGG, dropGO, emapplot, enrichDAVID, enrichGO, enrichKEGG, enrichMKEGG, enricher, geneID, geneInCategory, go2ont, go2term, gofilter, goplot, groupGO, gseGO, gseKEGG, gseMKEGG, gseaplot, gsfilter, heatplot, idType, ko2name, merge_result, plotGOgraph, read.gmt, ridgeplot, search_kegg_organism, setReadable, uniprot_get ExportMethods: simplify, dotplot ExportClasses: groupGOResult, compareClusterResult Package: clusterSeq Exports: kCluster, associatePosteriors, plotCluster, makeClusters, makeClustersFF, wallace Package: ClusterSignificance Exports: permute ExportMethods: show, pvalue, plot, permute, pcp, mlp, initialize, getData, conf.int, classify, c ExportClasses: PermutationResults, Pcp, Mlp, ClassifiedPoints Package: clusterStab ExportMethods: ecdf, hist, benhur, clusterComp ExportClasses: BenHur, ClusterComp Package: CMA Exports: GenerateLearningsets, ttest, welchtest, wilcoxtest, ftest, kruskaltest, limmatest, golubcrit, rfe ExportMethods: show, summary, toplist, plot, best, boxplot, ftable, roc, obsinfo, GeneSelection, tune, classification, join, evaluation, compare, Planarplot, ldaCMA, svmCMA, shrinkldaCMA, scdaCMA, rfCMA, qdaCMA, pnnCMA, pls_rfCMA, pls_lrCMA, pls_ldaCMA, plrCMA, pknnCMA, knnCMA, nnetCMA, LassoCMA, ElasticNetCMA, compBoostCMA, gbmCMA, dldaCMA, fdaCMA, flexdaCMA, prediction, weighted.mcr, wmc ExportClasses: learningsets, cloutput, varseloutput, clvarseloutput, genesel, evaloutput, predoutput, tuningresult Package: cn.farms Exports: cn.farms, cnLibrary, combineData, createAnnotation, createMatrix, distributionDistance, dnaCopySf, fragLengCorr, mlSummarization, normalizeAverage, normalizeCels, normalizeNpData, normalizeSequenceEffect, plotDendrogram, plotDensity, plotEvalIc, plotRegions, plotSmoothScatter, plotViolines, slSummarization, sparseFarmsC, summarizeFarmsExact, summarizeFarmsExact2, summarizeFarmsExact3, summarizeFarmsGaussian, summarizeFarmsMethods, summarizeFarmsStatistics, summarizeFarmsVariational, summarizeWindowBps, summarizeWindowMethods, summarizeWindowStd Package: cn.mops Exports: cn.mops, exomecn.mops, getReadCountsFromBAM, getSegmentReadCountsFromBAM, haplocn.mops, normalizeChromosomes, normalizeGenome, referencecn.mops, segment, singlecn.mops ExportMethods: show, segplot, segmentation, sampleNames, posteriorProbs, plot, params, normalizedData, makeRobustCNVR, localAssessments, integerCopyNumber, iniCall, individualCall, gr, cnvs, cnvr, calcIntegerCopyNumbers, calcFractionalCopyNumbers ExportClasses: CNVDetectionResult Package: CNAnorm Exports: dataFrame2object, CNAnormWorkflow ExportMethods: gcNorm, chrs, arms, pos, chrs<-, pos<-, ratio, ratio.n, ratio.s, ratio.s.n, segMean, segMean.n, addSmooth, addDNACopy, plotPeaks, plotGenome, peakPloidy, sugg.ploidy, sugg.peaks, valid.ploidy, valid.peaks, validation, exportTable, discreteNorm ExportClasses: CNAnorm, InData, DerivData, Params Package: CNEr Exports: reverseCigar, binFromCoordRange, binRangesFromCoordRange, binRestrictionString, readCNERangesFromSQLite, fetchChromSizes, Axt, makeAxtTracks, psubAxt, CNE, GRangePairs, readBed, readAxt, axtInfo, writeAxt, read.rmMask.GRanges, saveCNEToSQLite, read.rmskFasta, blatCNE, lastz, lavToPsl, scoringMatrix, axtChain, chainMergeSort, chainPreNet, chainNetSyntenic, netToAxt, lastal, makeGRBs, readAncora, readAncoraIntoSQLite, makeCNEDensity, makeAncoraFiles, CNEDensity, plotCNEWidth, plotCNEDistribution, N50, N90 ExportMethods: targetRanges, queryRanges, targetSeqs, querySeqs, symCount, subAxt, matchDistribution, fixCoordinates, CNE12, CNE21, thresholds, CNEMerged, CNEFinal, swap, ceScan, cneMerge, c, score, seqnames, strand, first, last, second, grglist, seqinfo, unique, syntenicDotplot, summary ExportClasses: Axt, CNE, GRangePairs Package: CNORdt Exports: simulatorDT, getFitDT, gaBinaryDT, cutAndPlotResultsDT, computeScoreDT, convert2array Package: CNORfeeder Exports: Binference, gaBinaryT1W, linksRanking, makeBTables, mapBTables2model, mapDDN2model, MIinference, weighting Package: CNORfuzzy Exports: CNORwrapFuzzy, computeScoreFuzzy, compileMultiRes, defaultParametersFuzzy, gaDiscreteT1, getRefinedModel, interpretDiscreteGA, plotMeanFuzzyFit, prep4simFuzzy, reduceFuzzy, simFuzzyT1, writeFuzzyNetwork Package: CNORode Exports: createLBodeContPars, defaultParametersGA, defaultParametersSSm, getLBodeContObjFunction, getLBodeDataSim, getLBodeMINLPObjFunction, getLBodeModelSim, getLBodeSimFunction, getStates, incidence2Adjacency, minlpLBodeSSm, parEstimationLBodeGA, parEstimationLBode, parEstimationLBodeSSm, plotLBodeFitness, plotLBodeModelSim, simdata2cnolist, simulate Package: CNTools Exports: diffBy, CNSeg ExportMethods: getRS, segBy, rs, genefilter, getCor, rs<-, getDist, segList<-, show, segList, madFilter ExportClasses: CNSeg, RS Package: CNVfilteR Exports: filterCNVs, loadCNVcalls, loadSNPsFromVCF, loadVCFs, plotAllCNVs, plotScoringModel, plotVariantsForCNV Package: cnvGSA Exports: f.readConfig, cnvGSAlogRegTest, cnvGSAgsTables, cnvGSAIn, f.enrFiles, f.makeViz, CnvGSAInput, config.ls, config.ls<-, params.ls, params.ls<-, cnvData.ls, cnvData.ls<-, phData.ls, phData.ls<-, gsData.ls, gsData.ls<-, geneID.ls, geneID.ls<-, CnvGSAOutput, res.ls, gsTables.ls ExportMethods: config.ls, config.ls<-, params.ls, params.ls<-, cnvData.ls, cnvData.ls<-, phData.ls, phData.ls<-, gsData.ls, gsData.ls<-, geneID.ls, geneID.ls<-, res.ls, gsTables.ls ExportClasses: CnvGSAOutput, CnvGSAInput Package: CNVPanelizer Exports: IndexMultipleBams, NormalizeCounts, Background, ReportTables, BedToGenomicRanges, ReadCountsFromBam, BootList, PlotBootstrapDistributions, CombinedNormalizedCounts, SelectReferenceSetFromReadCounts, SelectReferenceSetByPercentil, SelectReferenceSetByInterquartileRange, SelectReferenceSetByKmeans, CNVPanelizer, CNVPanelizerFromReadCountsHELPER, CNVPanelizerFromReadCounts, CollectColumnFromAllReportTables, StatusHeatmap, WriteListToXLSX, ReadXLSXToList, RunCNVPanelizerShiny Package: CNVRanger Exports: cnvEQTL, cnvGWAS, generateGDS, importLrrBaf, plotEQTL, plotManhattan, plotRecurrentRegions, populationRanges, setupCnvGWAS Package: CNVrd2 Exports: calculateLDSNPandCNV, groupBayesianCNVs ExportMethods: countReadInWindow, emnormalCNV, groupCNVs, plotCNVrd2, searchGroupCNVs, segmentSamples, segmentSamplesUsingPopInformation, identifyPolymorphicRegion, plotPolymorphicRegion ExportClasses: clusteringCNVs, CNVrd2, numericOrNULL Package: CNVtools Exports: CNVtest.select.model, CNVtest.binary, CNVtest.binary.T, CNVtest.qt, CNVtest.qt.T, apply.pca, apply.ldf, cnv.plot, qt.plot, getQualityScore, compact.data.frame, get.model.spec, CNV.fitModel Package: cobindR Exports: read.transfac.pfm, generate.background, cobindr, seqObj, cobindRConfiguration ExportMethods: detrending, find.pairs, get.bindingsite.ranges, plot.detrending, plot.gc, plot.pairdistance, plot.positionprofile, plot.positions, plot.positions.simple, plot.tfbs.heatmap, plot.tfbs.venndiagram, plot.tfbslogo, predicted2pwm, rtfbs, search.gadem, search.pwm, testCpG, write.bindingsites, write.bindingsites.table, get.pairs, write.sequences, get.significant.pairs, uid, name, sequences, bg_sequences, desc, configuration, pfm, binding_sites, bg_binding_sites, pairs, bg_pairs, pairs_of_interest, species, location, comment, sequence, experiment_description, id, sequence_source, sequence_origin, sequence_type, bg_sequence_source, bg_sequence_type, bg_sequence_origin, downstream, upstream, max_distance, pfm_path, threshold, fdrThreshold, path, mart, pseudocount, pValue ExportClasses: cobindr, configuration, SeqObj Package: CoCiteStats Exports: actorAdjTable, gene.geneslist.sig, gene.geneslist.statistic, gene.gene.statistic, paperLen, twowayTable, twTStats Package: COCOA Exports: aggregateSignal, aggregateSignalGRList, convertToFromNullDist, getGammaPVal, getMetaRegionProfile, getPermStat, getTopRegions, regionQuantileByTargetVar, rsRankingIndex, rsScoreHeatmap, runCOCOA, runCOCOAPerm, signalAlongAxis Package: codelink Exports: readCodelink, writeCodelink, reportCodelink, plotMA, plotCorrelation, plotDensities, plotCV, imageCodelink, bkgdCorrect, normalize, mergeArray, createWeights, arrayNew, selCV, cutCV, fc2Cond, na2false, logCodelink, readCodelinkSet, Codelink2CodelinkSet ExportMethods: [, show, summary, summaryFlag, annotation, codCorrect, codNormalize, codPreprocess, probeNames, probeTypes, getSNR, getInt, getBkg, getInfo, getWeight, getFlag, meanSNR, codPlot, exprs, chipDevice, filterSNR, codUniverse, writeCluster, writeCodelink, averageProbes ExportClasses: Codelink, CodelinkSet, CodelinkSetUnique Package: CODEX Exports: segment, qc, normalize, getmapp, getcoverage, getbambed, choiceofK, getgc, normalize2 Package: coexnet Exports: CCP, cofVar, createNet, difExprs, exprMat, findThreshold, geneSymbol, getAffy, getInfo, ppiNet, sharedComponents Package: CoGAPS Exports: CoGAPS, CogapsParams, GWCoGAPS, binaryA, buildReport, calcCoGAPSStat, calcZ, checkpointsEnabled, compiledWithOpenMPSupport, findConsensusMatrix, getClusteredPatterns, getCorrelationToMeanPattern, getFeatureLoadings, getMeanChiSq, getOriginalParameters, getParam, getRetinaSubset, getSampleFactors, getSubsets, getUnmatchedPatterns, getVersion, patternMarkers, plotPatternMarkers, plotResiduals, reconstructGene, scCoGAPS, setAnnotationWeights, setDistributedParams, setFixedPatterns, setParam ExportClasses: CogapsResult, CogapsParams Package: cogena Exports: PEI, clEnrich, clEnrich_one, coExp, corInCluster, enrichment, gene2set, geneExpInCluster, geneInCluster, gmt2list, gmtlist2file, heatmapCluster, heatmapCmap, heatmapPEI, logfc, sota, upDownGene ExportMethods: summary, show, nClusters, mat, geneclusters, clusterMethods ExportClasses: genecl, cogena Package: coGPS Exports: PCOPA, PatientSpecificGeneList, PlotTopPCOPA, plotCOPA, permCOPA Package: COHCAP Exports: COHCAP.annotate, COHCAP.qc, COHCAP.site, COHCAP.avg.by.site, COHCAP.avg.by.island, COHCAP.integrate.avg.by.site, COHCAP.integrate.avg.by.island, COHCAP.denovo, COHCAP.reformatFinalReport, COHCAP.BSSeq.preprocess, COHCAP.BSSeq_V2.methyl.table Package: cola Exports: [.ConsensusPartitionList, [.HierarchicalPartition, [[.ConsensusPartitionList, [[.HierarchicalPartition, dim.ConsensusPartition, dim.ConsensusPartitionList, dim.HierarchicalPartition, ATC, FCC, PAC, aPAC, adjust_matrix, adjust_outlier, all_partition_methods, all_top_value_methods, cola, cola_opt, concordance, consensus_partition, correspond_between_rankings, correspond_between_two_rankings, find_best_km, get_hierarchy, hierarchical_partition, knitr_add_tab_item, knitr_insert_tabs, map_to_entrez_id, recalc_stats, register_NMF, register_SOM, register_partition_methods, register_top_value_methods, relabel_class, remove_partition_methods, remove_top_value_methods, run_all_consensus_partition_methods, submit_to_david, test_between_factors, top_elements_overlap, ConsensusPartition, ConsensusPartitionList, HierarchicalPartition ExportMethods: top_rows_overlap, top_rows_heatmap, test_to_known_factors, suggest_best_k, select_partition_number, rownames, plot_ecdf, nrow, ncol, membership_heatmap, max_depth, is_stable_k, is_best_k, get_stats, get_signatures, get_param, get_membership, get_matrix, get_consensus, get_classes, get_anno_col, get_anno, dimension_reduction, consensus_heatmap, compare_signatures, colnames, collect_stats, collect_plots, collect_classes, cola_report, all_nodes, all_leaves, GO_enrichment ExportClasses: HierarchicalPartition, ConsensusPartitionList, ConsensusPartition Package: coMET Exports: comet, comet.web, comet.list, chrUCSC2ENSEMBL, gcContent_UCSC, GWAScatalog_UCSC, GAD_UCSC, GeneReviews_UCSC, refGenes_UCSC, xenorefGenes_UCSC, knownGenes_UCSC, genesName_ENSEMBL, genes_ENSEMBL, interestGenes_ENSEMBL, transcript_ENSEMBL, interestTranscript_ENSEMBL, snpBiomart_ENSEMBL, snpLocations_UCSC, structureBiomart_ENSEMBL, ClinVarCnv_UCSC, ClinVarMain_UCSC, CoreillCNV_UCSC, COSMIC_UCSC, chromatinHMMAll_UCSC, chromatinHMMOne_UCSC, HistoneAll_UCSC, HistoneOne_UCSC, cpgIslands_UCSC, DNAse_UCSC, regulationBiomart_ENSEMBL, bindingMotifsBiomart_ENSEMBL, regulatorySegmentsBiomart_ENSEMBL, regulatoryFeaturesBiomart_ENSEMBL, otherRegulatoryRegionsBiomart_ENSEMBL, regulatoryEvidenceBiomart_ENSEMBL, miRNATargetRegionsBiomart_ENSEMBL, repeatMasker_UCSC, segmentalDups_UCSC, chromHMM_RoadMap, DNaseI_RoadMap, dgfootprints_RoadMap, eQTL_GTEx, imprintedGenes_GTEx, psiQTL_GTEx, metQTL, eQTL, TFBS_FANTOM, DNaseI_FANTOM, ChIPTF_ENCODE, HiCdata2matrix Package: compartmap Exports: fisherZ, getABSignal, getATACABsignal, getArrayABsignal, getBinMatrix, getCompartments, getCorMatrix, ifisherZ, plotAB Package: COMPASS Exports: COMPASSDescription<-, metadata<-, COMPASS, COMPASSContainer, COMPASSContainerFromGatingSet, COMPASSDescription, COMPASSfitToCountsTable, CellCounts, Combinations, FunctionalityScore, GetThresholdedIntensities, PolyfunctionalityScore, Posterior, PosteriorDiff, PosteriorLogDiff, PosteriorPs, PosteriorPu, Response, SimpleCOMPASS, TotalCellCounts, UniqueCombinations, categories, getCounts, markers, metadata, pheatmap, plot2, plotCOMPASSResultStack, scores, select_compass_pops, shinyCOMPASS, shinyCOMPASSDeps, translate_marker_names, transpose_list Package: compcodeR Exports: DESeq.GLM.createRmd, DESeq.nbinom.createRmd, DESeq2.createRmd, DSS.createRmd, EBSeq.createRmd, NBPSeq.createRmd, NOISeq.prenorm.createRmd, TCC.createRmd, baySeq.createRmd, checkDataObject, checkTableConsistency, check_compData, check_compData_results, compData, convertListTocompData, convertcompDataToList, edgeR.GLM.createRmd, edgeR.exact.createRmd, generateCodeHTMLs, generateSyntheticData, listcreateRmd, logcpm.limma.createRmd, runComparison, runComparisonGUI, runDiffExp, sqrtcpm.limma.createRmd, summarizeSyntheticDataSet, ttest.createRmd, voom.limma.createRmd, voom.ttest.createRmd, vst.limma.createRmd, vst.ttest.createRmd ExportClasses: compData Package: compEpiTools ExportMethods: GRangesInPromoters, GRannotate, GRbaseCoverage, GRcoverage, GRcoverageInbins, GRcoverageSummit, GRmidpoint, countOverlapsInBins, distanceFromTSS, enhancers, featuresLength, getPromoterClass, GRanges2ucsc, GRannotateSimple, GRenrichment, GRsetwidth, makeGtfFromDb, matchEnhancers Package: CompGO Exports: annotateBedFromDb, getFnAnot_genome, zTransformDirectory, doZtrans.single, slidingJaccard, plotZScores, plotPairwise, plotTwoGODags, plotZRankedDAG, compareZscores, viewKegg, plotInteractive, PCAplot, plotDendrogram Package: ComplexHeatmap Exports: +.AdditiveUnit, [.AnnotationFunction, [.Heatmap, [.HeatmapAnnotation, [.HeatmapList, [.SingleAnnotation, [.comb_mat, c.ColorMapping, c.HeatmapAnnotation, dim.Heatmap, grid.draw.Legends, height.AnnotationFunction, height.Heatmap, height.HeatmapAnnotation, height.HeatmapList, height.Legends, height.SingleAnnotation, height<-.AnnotationFunction, height<-.HeatmapAnnotation, height<-.SingleAnnotation, heightDetails.annotation_axis, heightDetails.legend, heightDetails.legend_body, heightDetails.packed_legends, length.HeatmapAnnotation, length.HeatmapList, names.HeatmapAnnotation, names.HeatmapList, names<-.HeatmapAnnotation, ncol.Heatmap, nobs.AnnotationFunction, nobs.HeatmapAnnotation, nobs.SingleAnnotation, nrow.Heatmap, print.comb_mat, size.AnnotationFunction, size.HeatmapAnnotation, size.SingleAnnotation, size<-.AnnotationFunction, size<-.HeatmapAnnotation, size<-.SingleAnnotation, str.comb_mat, summary.Heatmap, summary.HeatmapList, t.comb_mat, width.AnnotationFunction, width.Heatmap, width.HeatmapAnnotation, width.HeatmapList, width.Legends, width.SingleAnnotation, width<-.AnnotationFunction, width<-.HeatmapAnnotation, width<-.SingleAnnotation, widthDetails.annotation_axis, widthDetails.legend, widthDetails.legend_body, widthDetails.packed_legends, %v%, AdditiveUnit, AnnotationFunction, ColorMapping, Heatmap, HeatmapAnnotation, HeatmapList, Legend, Legends, SingleAnnotation, UpSet, adjust_dend_by_x, anno_barplot, anno_block, anno_boxplot, anno_density, anno_empty, anno_histogram, anno_horizon, anno_image, anno_joyplot, anno_lines, anno_link, anno_mark, anno_oncoprint_barplot, anno_points, anno_simple, anno_summary, anno_text, anno_zoom, annotation_axis_grob, cluster_within_group, columnAnnotation, comb_degree, comb_name, comb_size, decorate_annotation, decorate_column_dend, decorate_column_names, decorate_column_title, decorate_dend, decorate_dimnames, decorate_heatmap_body, decorate_row_dend, decorate_row_names, decorate_row_title, decorate_title, default_axis_param, default_get_type, dend_heights, dend_xy, dendrogramGrob, densityHeatmap, dist2, extract_comb, getXY_in_parent_vp, grid.annotation_axis, grid.boxplot, grid.dendrogram, ht_global_opt, ht_opt, is_abs_unit, list_components, list_to_matrix, make_comb_mat, max_text_height, max_text_width, merge_dendrogram, normalize_comb_mat, oncoPrint, order.comb_mat, packLegend, pindex, restore_matrix, rowAnnotation, row_anno_barplot, row_anno_boxplot, row_anno_density, row_anno_histogram, row_anno_link, row_anno_points, row_anno_text, set_name, set_size, smartAlign2, subset_gp, subset_matrix_by_row, subset_vector, test_alter_fun, unify_mat_list, upset_right_annotation, upset_top_annotation, AdditiveUnit, AnnotationFunction, ColorMapping, Heatmap, HeatmapAnnotation, HeatmapList, Legends, SingleAnnotation ExportMethods: set_component_width, set_component_height, row_order, row_dend, re_size, prepare, map_to_colors, make_row_cluster, make_layout, make_column_cluster, heatmap_legend_size, get_legend_param_list, get_color_mapping_list, draw_title, draw_heatmap_list, draw_heatmap_legend, draw_heatmap_body, draw_dimnames, draw_dend, draw_annotation_legend, draw_annotation, draw, copy_all, component_width, component_height, column_order, column_dend, color_mapping_legend, annotation_legend_size, adjust_heatmap_list, add_heatmap ExportClasses: SingleAnnotation, Legends, HeatmapList, HeatmapAnnotation, Heatmap, ColorMapping, AnnotationFunction, AdditiveUnit Package: CONFESS Exports: FluoSelection_byRun, Fluo_CV_modeling, Fluo_CV_prep, Fluo_adjustment, Fluo_inspection, Fluo_modeling, Fluo_ordering, LocationMatrix, cluster2outlier, createFluo, defineLocClusters, getFluo, getFluo_byRun, pathEstimator, readFiles, simcells, spotEstimator Package: consensus Exports: MultiMeasure, fitConsensus, plotOneFit, plotMarginals, plotMostDiscordant Package: ConsensusClusterPlus Exports: ConsensusClusterPlus, calcICL Package: consensusDE Exports: buildSummarized, diag_plots, multi_de_pairs Package: consensusOV Exports: get.bentink.subtypes, get.consensus.subtypes, get.hao.subtypes, get.helland.subtypes, get.konecny.subtypes, get.subtypes, get.verhaak.subtypes, margin Package: consensusSeekeR Exports: findConsensusPeakRegions, readNarrowPeakFile Package: contiBAIT Exports: BAIT, ChrTable, ContigOrdering, LibraryGroupList, LinkageGroupList, StrandFreqMatrix, StrandReadMatrix, StrandStateList, StrandStateMatrix, barplotLinkageGroupCalls, clusterContigs, contiBAIT, findSexGroups, findSimilarLibraries, fixLinkageGroups, flipOrderedLinkageGroups, highlightAssemblyErrors, ideogramPlot, locateMisorients, makeBoxPlot, makeChrTable, mapGapFromOverlap, mergeFlankedLGs, orderAllLinkageGroups, plotContigOrder, plotLGDistances, plotWCdistribution, preprocessStrandTable, reorientAndMergeLGs, strandSeqFreqTable, thoroughBed, writeBed ExportMethods: writeBed, thoroughBed, show, reorientAndMergeLGs, preprocessStrandTable, plotWCdistribution, plotLGDistances, plotContigOrder, orderAllLinkageGroups, mergeFlankedLGs, makeBoxPlot, locateMisorients, ideogramPlot, flipOrderedLinkageGroups, fixLinkageGroups, findSimilarLibraries, findSexGroups, clusterContigs, barplotLinkageGroupCalls ExportClasses: StrandStateMatrix, StrandStateList, StrandReadMatrix, StrandFreqMatrix, LinkageGroupList, LibraryGroupList, ContigOrdering, ChrTable Package: conumee Exports: CNV.bin, CNV.create_anno, CNV.detail, CNV.detailplot, CNV.detailplot_wrap, CNV.fit, CNV.genomeplot, CNV.load, CNV.process, CNV.segment, CNV.write, read.450k.url ExportMethods: show, names, coef, names<-, [ ExportClasses: CNV.data, CNV.anno, CNV.analysis Package: copa Exports: copa, plotCopa, copaPerm, tableCopa, scatterPlotCopa, summaryCopa Package: copynumber Exports: winsorize, multipcf, pcf, aspcf, plotChrom, plotGenome, plotSample, plotAllele, plotFreq, plotHeatmap, plotGamma, plotAberration, imputeMissing, subsetData, subsetSegments, selectSegments, plotCircle, callAberrations, interpolate.pcf, pcfPlain, getGRangesFormat Package: CopyNumberPlots Exports: EnsemblStyle, UCSCStyle, Ztree2Hclust, colByCopyNumber, computeHclustPlotOrder, getBAFColumn, getChrColumn, getColumn, getCopyNumberColors, getCopyNumberColumn, getEndColumn, getIDColumn, getLOHColumn, getLRRColumn, getPosColumn, getSegmentValueColumn, getStartColumn, loadCopyNumberCalls, loadCopyNumberCallsCNVkit, loadCopyNumberCallsCnmops, loadCopyNumberCallsDECoN, loadCopyNumberCallsDNAcopy, loadCopyNumberCallsPanelcnmops, loadCopyNumberCallsSeg, loadCopyNumberCallspennCNV, loadSNPData, loadSNPDataDNAcopy, loadSNPDataFromVCF, plotBAF, plotCopyNumberCalls, plotCopyNumberCallsAsLines, plotCopyNumberSummary, plotLRR, plotSingleCellCopyNumberCalls, plotSingleCellCopyNumberSummary, prepareLabels, readHDF5Ztree, removeNAs, transformChr Package: coRdon Exports: B, Bplot, CAI, E, ENC, ENCprime, Fop, GCB, MCB, MELP, MILC, SCUO, codonCounts, codonTable, contable, crossTab, enrichBarplot, enrichMAplot, enrichMatrix, enrichment, getCOG, getID, getKO, getSeqAnnot, getVariable, getlen, intraBplot, readSet, reduceCrossTab, setCOG, setKO ExportMethods: show, length, [[, [ Package: CoRegFlux Exports: ODCurveToFluxCurves, ODCurveToMetabolicGeneCurves, Simulation, adjust_constraints_to_observed_rates, build_exchange_met, coregflux_static, get_biomass_flux_position, get_fba_fluxes_from_observations, get_fva_intervals_from_observations, get_metabolites_exchange_fluxes, predict_linear_model_influence, update_fluxes_constraints_geneKOOV, update_fluxes_constraints_influence, visFluxCurves, visMetabolicGeneCurves Package: CoRegNet Exports: discretizeExpressionData, coregnet, hLICORN, masterRegulator, display ExportMethods: print, show, length, dim, summary, regulatorInfluence, addEvidences, coregulators, coerce, regulators, targets, activators, repressors, coregnetToList, coregnetToDataframe, addCooperativeEvidences, refine ExportClasses: coregnet Package: Cormotif Exports: cormotiffit, cormotiffitall, cormotiffitfull, cormotiffitsep, generank, plotIC, plotMotif Package: CorMut Exports: seqFormat, kaksCodon, kaksAA, ckaksCodon, ckaksAA, miCodon, miAA, jiAA, biCkaksCodon, biCkaksAA, biMICodon, biMIAA, biJIAA, seq_num.CorMut, kaks.CorMut, lod.CorMut, q.CorMut, ka.CorMut, ks.CorMut, mi.CorMut, p.value.CorMut, ckaks.CorMut, method.CorMut, positiveSite01.CorMut, positiveSite02.CorMut, state_1.CorMut, statistic_1.CorMut, state_2.CorMut, statistic_2.CorMut ExportMethods: filterSites, plot, biCompare ExportClasses: kaksCodon, kaksAA, ckaks, MI, biCkaksCodon, biCkaksAA, biMICodon, biMIAA, biJIAA Package: CORREP Exports: cor.balance, cor.bootci, cor.LRtest, cor.LRtest.std, cor.unbalance, permutest Package: coseq Exports: ICL, NormMixClus, NormMixClusK, NormMixParam, clusterEntropy, clusterInertia, clusters, compareARI, compareICL, convertLegacyCoseq, coseq, coseqFullResults, coseqGlobalPlots, coseqModelPlots, coseqResults, coseqRun, kmeansProbaPost, likelihood, logclr, matchContTable, model, nbCluster, plot, proba, profiles, tcounts, transformRNAseq, transformationType ExportMethods: transformationType, tcounts, summary, show, profiles, proba, plot, nbCluster, model, likelihood, coseqFullResults, coseq, compareARI, clusters, ICL, Djumpextract, DDSEextract ExportClasses: coseqResults Package: cosmiq Exports: combine_spectra, create_datamatrix, peakdetection, retention_time, cosmiq, eicmatrix, quantify_combined Package: CountClust Exports: BatchCorrectedCounts, ExtractHighCorFeatures, ExtractTopFeatures, FitGoM, RemoveSparseFeatures, StructureGGplot, compGoM, compare_omega, handleNA, nullmodel_GoM Package: countsimQC Exports: countsimQCReport, generateIndividualPlots Package: covEB Exports: covEB, EBsingle Package: CoverageView Exports: export.wig, write.profile ExportMethods: cov.interval, cov.matrix, draw.heatmap, draw.profile, genome.covplot.cumdepth, genome.covplot.depth ExportClasses: CoverageBamFile, CoverageBigWigFile Package: covRNA Exports: stat, ord, vis, plot.stat, plot.ord Package: cpvSNP Exports: assocPvalBySetPlot, createArrayData, geneToSNPList, glossi, glossiMarginal, plotPvals, simulate_chisq, vegas, vegasMarginal ExportMethods: geneSetName, pValue, simulatedStats, degreesOfFreedom, statistic ExportClasses: GeneSetResult, GeneSetResultCollection, VEGASResult, VEGASResultCollection, GLOSSIResult, GLOSSIResultCollection Package: cqn Exports: cqn, cqn.fixedlength, cqnplot Package: CRImage Exports: labelCells, SauvolaThreshold, plotCorrectedCN, correctCopyNumber, calculateOtsu, convertLABToRGB, convertRGBToLAB, convertHSVToRGB, convertRGBToHSV, colorCorrection, calculateMeanStdTarget, createBinaryImage, segmentImage, createClassifier, classifyCells, calculateCellularity, processAperio Package: CRISPRseek Exports: offTargetAnalysis, filterOffTarget, filtergRNAs, findgRNAs, searchHits2, writeHits2, searchHits, writeHits, translatePattern, getOfftargetScore, buildFeatureVectorForScoring, compare2Sequences, calculategRNAEfficiency, annotateOffTargets, isPatternUnique, uniqueREs Package: crisprseekplus Exports: cspServer, cspUI, disableDownload, fileInputFunc, getLoadingMsg, getLogo, installpack, startcrisprseekplus, trueFalseFunc Package: CrispRVariants Exports: CrisprRun, CrisprSet, abifToFastq, alleles, alns, barplotAlleleFreqs, consensusSeqs, countDeletions, countIndels, countInsertions, findChimeras, findSNVs, getChimeras, mutationEfficiency, narrowAlignments, plotAlignments, plotChimeras, plotFreqHeatmap, plotVariants, readsByPCRPrimer, readsToTarget, readsToTargets, refFromAlns, variantCounts ExportMethods: mergeCrisprSets, indelPercent ExportClasses: CrisprSet, CrisprRun Package: CrossICC Exports: CrossICC, CrossICCInput, predictor, ssGSEA, summaryCrossICC Package: crossmeta Exports: add_sources, contribute, diff_expr, diff_path, es_meta, explore_paths, format_fdrs, get_raw, load_diff, load_path, load_raw, path_meta, setup_prev, symbol_annot, which_max_iqr Package: csaw Exports: asDGEList, calculateCPM, checkBimodality, clusterFDR, clusterWindows, clusterWindowsList, combineOverlaps, combineTests, controlClusterFDR, correlateReads, csawUsersGuide, detailRanges, empiricalFDR, empiricalOverlaps, extractReads, filterWindowsControl, filterWindowsGlobal, filterWindowsLocal, filterWindowsProportion, findMaxima, findOverlapsList, getBestOverlaps, getBestTest, getPESizes, getWidths, maximizeCcf, mergeResults, mergeResultsList, mergeWindows, mergeWindowsList, mixedClusters, mixedOverlaps, normFactors, normOffsets, overlapResults, overlapResultsList, profileSites, readParam, reform, regionCounts, scaleControlFilter, scaledAverage, strandedCounts, summitOverlaps, upweightSummit, windowCounts, wwhm ExportMethods: show, reform, asDGEList, $ ExportClasses: readParam Package: CSSP Exports: bindcount, bindcount.chr, callpeak, createBinData, cssp.fit, cssp.power, cssp.sim, fit.freq, pBBT, peakcount, peakcount.chr, qBBT, readBinFile, tag2bin, tag2bin.chr ExportClasses: CSSPFit, BinData Package: ctc Exports: hc2Newick, hclust2treeview, r2cdt, r2atr, r2gtr, r2cluster, r2xcluster, read.eisen, xcluster, xcluster2r Package: cTRAP Exports: analyseDrugSetEnrichment, convertENSEMBLtoGeneSymbols, downloadENCODEknockdownMetadata, filterCMapMetadata, getCMapConditions, getCMapPerturbationTypes, loadCMapData, loadCMapZscores, loadDrugDescriptors, loadENCODEsamples, loadExpressionDrugSensitivityAssociation, parseCMapID, performDifferentialExpression, plotDrugSetEnrichment, plotTargetingDrugsVSsimilarPerturbations, predictTargetingDrugs, prepareCMapPerturbations, prepareDrugSets, prepareENCODEgeneExpression, rankSimilarPerturbations Package: ctsGE Exports: ClustIndexes, PlotIndexesClust, PreparingTheIndexes, ctsGEShinyApp, index, readTSGE Package: cummeRbund Exports: readCufflinks, JSdist, JSdistVec, JSdistFromP, shannon.entropy, makeprobs, makeprobsvec, csClusterPlot ExportMethods: runInfo, varModel, annotation, genes, isoforms, TSS, CDS, promoters, splicing, relCDS, fpkm, repFpkm, count, distValues, csDensity, csScatter, csVolcano, csBoxplot, csHeatmap, csFoldChangeHeatmap, csDistHeat, csCluster, csDendro, MAplot, dispersionPlot, csSpecificity, fpkmMatrix, repFpkmMatrix, countMatrix, repCountMatrix, diffData, diffTable, features, featureNames, samples, replicates, expressionPlot, expressionBarplot, getGene, getGenes, getFeatures, getGeneId, findGene, getSig, getSigTable, addFeatures, getLevels, getRepLevels, findSimilar, makeRnk, genePlot, makeGeneRegionTrack, DB, sigMatrix, csScatterMatrix, csVolcanoMatrix, MDSplot, PCAplot, fpkmSCVPlot, csNMF, conditions, csPie ExportClasses: CuffSet, CuffData, CuffDist, CuffFeature, CuffFeatureSet, CuffGene, CuffGeneSet Package: customProDB Exports: PrepareAnnotationEnsembl, PrepareAnnotationRefseq, easyRun, easyRun_mul, calculateRPKM, Outputproseq, InputVcf, Varlocation, Positionincoding, aaVariation, OutputVarproseq, OutputVarproseq_single, OutputVarprocodingseq, Outputaberrant, Bed2Range, JunctionType, OutputNovelJun, OutputsharedPro, Multiple_VCF, SharedJunc Package: cycle Exports: ar1analysis, backgroundData, fdrfourier, fourierscore Package: cydar Exports: cellAssignments, cellInformation, cellIntensities, countCells, createColorBar, dnaGate, expandRadius, findFirstSphere, getCenterCell, intensities, intensityRanges, interpretSpheres, labelSpheres, medIntensities, multiIntHist, neighborDistances, normalizeBatch, outlierGate, pickBestMarkers, plotSphereIntensity, plotSphereLogFC, poolCells, prepareCellData, spatialFDR ExportMethods: show, markernames, intensities, cellAssignments, cbind, [<-, [ ExportClasses: CyData Package: CytoDx Exports: CytoDx.fit, CytoDx.pred, fcs2DF, meanUnique, pRank, rank.ub.average, set2DF, treeGate Package: cytofast Exports: cellCounts, cfList, counts, cytoBoxplots, cytoHeatmaps, cytottest, drawTree, expr, msiPlot, readCytosploreFCS, results, samples ExportClasses: cfList Package: CytoML Exports: CytoML.par.get, CytoML.par.set, GatingSet2cytobank, GatingSet2flowJo, ce_get_cmpensations, ce_get_transformations, closeWorkspace, cytobank2GatingSet, cytobankExperiment, cytobank_to_gatingset, diva_get_sample_groups, diva_get_samples, diva_to_gatingset, extend, fj_ws_get_keywords, fj_ws_get_sample_groups, fj_ws_get_samples, flowjo_to_gatingset, flowjo_ws_close, gatingset_to_cytobank, gatingset_to_flowjo, getFJWSubsetIndices, getKeywords, getSampleGroups, getSamples, gs_compare_cytobank_counts, openDiva, open_cytobank_experiment, open_diva_xml, open_flowjo_xml, parseWorkspace ExportMethods: show, sampleNames, parseWorkspace, pData, markernames, colnames, GatingSet ExportClasses: flowjo_workspace, diva_workspace Package: dada2 Exports: PacBioErrfun, addSpecies, assignSpecies, assignTaxonomy, collapseNoMismatch, dada, derepFastq, fastqFilter, fastqPairedFilter, filterAndTrim, getDadaOpt, getErrors, getSequences, getUniques, inflateErr, isBimera, isBimeraDenovo, isBimeraDenovoTable, isPhiX, isShiftDenovo, learnErrors, loessErrfun, makeSequenceTable, mergePairs, mergeSequenceTables, noqualErrfun, nwalign, nwhamming, plotComplexity, plotErrors, plotQualityProfile, rc, removeBimeraDenovo, removePrimers, seqComplexity, setDadaOpt, uniquesToFasta Package: dagLogo Exports: addScheme, buildBackgroundModel, cleanPeptides, colorsets, dagHeatmap, dagLogo, fetchSequence, formatSequence, getGroupingSymbol, prepareProteome, prepareProteomeByFTP, prepareProteomeByUniProtWS, testDAU ExportClasses: testDAUresults, dagPeptides, dagBackground, Proteome Package: daMA Exports: analyseMA, cinfo, cinfoB.AB, cmat, cmatB.AB, core, designMA, designs.basic, designs.composite Package: DaMiRseq Exports: DaMiR.Allplot, DaMiR.Clustplot, DaMiR.EnsembleLearning, DaMiR.FBest, DaMiR.FReduct, DaMiR.FSelect, DaMiR.FSort, DaMiR.MDSplot, DaMiR.SV, DaMiR.SVadjust, DaMiR.corrplot, DaMiR.goldenDice, DaMiR.normalization, DaMiR.sampleFilt, DaMiR.transpose, DaMiR.makeSE, DaMiR.EnsembleLearning2cl, DaMiR.EnsembleLearningNcl, DaMiR.EnsembleLearning2cl_Training, DaMiR.EnsembleLearning2cl_Test, DaMiR.EnsembleLearning2cl_Predict Package: DAPAR Exports: writeMSnsetToExcel, writeMSnsetToCSV, createMSnset, readExcel, listSheets, addOriginOfValue, saveParameters, rbindMSnset, boxPlotD, densityPlotD, wrapper.CVDistD, CVDistD, wrapper.corrMatrixD, corrMatrixD, wrapper.heatmapD, heatmapD, wrapper.mvPerLinesHisto, mvPerLinesHisto, wrapper.mvPerLinesHisto_HC, mvPerLinesHisto_HC, wrapper.mvPerLinesHistoPerCondition, mvPerLinesHistoPerCondition, wrapper.mvHisto, mvHisto, wrapper.pca, plotPCA_Eigen_hc, plotPCA_Var, plotPCA_Ind, wrapper.hc_mvTypePlot2, hc_mvTypePlot2, wrapper.mvImage, mvImage, heatmap.DAPAR, mvFilter, mvFilterFromIndices, mvFilterGetIndices, removeLines, deleteLinesFromIndices, StringBasedFiltering, getIndicesOfLinesToRemove, wrapper.normalizeD, wrapper.compareNormalizationD, compareNormalizationD, getListNbValuesInLines, reIntroduceMEC, findMECBlock, wrapper.impute.fixedValue, wrapper.impute.detQuant, wrapper.impute.slsa, getQuantile4Imp, wrapper.impute.KNN, wrapper.impute.mle, aggregateTopn, aggregateMean, aggregateSum, aggregateIterParallel, aggregateIter, BuildAdjacencyMatrix, GraphPepProt, BuildColumnToProteinDataset, BuildColumnToProteinDataset_par, getProteinsStats, limmaCompleteTest, check.design, check.conditions, Get_AllComparisons, wrapper.t_test_Complete, diffAnaVolcanoplot_rCharts, diffAnaSave, diffAnaComputeFDR, wrapperCalibrationPlot, hc_logFC_DensityPlot, getProcessingInfo, pepa.test, group_GO, enrich_GO, univ_AnnotDbPkg, GOAnalysisSave, scatterplotEnrichGO_HC, barplotEnrichGO_HC, barplotGroupGO_HC, my_hc_ExportMenu Package: DART Exports: DoDART, DoDARTCLQ, BuildRN, EvalConsNet, PruneNet, PredActScore Package: DBChIP Exports: DBChIP, read.binding.site.list, site.merge, load.data, get.site.count, test.diff.binding, report.peak, plotPeak Package: dcanr Exports: cor.pairs, dcAdjust, dcEvaluate, dcMethods, dcNetwork, dcPipeline, dcTest, getConditionNames, getSimData, getTrueNetwork, mi.ap, perfMethods, performanceMeasure, plotSimNetwork ExportMethods: dcScore Package: dcGSA Exports: LDcov, dcGSA, readGMT Package: DChIPRep Exports: DChIPRepResults, getMATfromDataFrame, importData, importDataFromMatrices, importData_soGGi, robust_mean, summarizeCountsPerPosition ExportMethods: show, runTesting, resultsDChIPRep, plotSignificance, plotProfiles, FDRresults, DESeq2Data, resultsDChIPRep<-, FDRresults<-, DESeq2Data<- ExportClasses: DChIPRepResults Package: ddCt Exports: exprs, assayData, phenoData, pData, phenoData<-, pData<-, featureData, fData, featureData<-, fData<-, varLabels, varMetadata, varMetadata<-, featureNames, featureNames<-, sampleNames, sampleNames<-, brewer.pal, brewer.pal.info, barchart, panel.barchart, panel.segments, panel.grid, panel.abline, panel.text, xtable, QuantStudioFrame, readQuantStudio, SDMFrame, readSDM, TSVFrame, barploterrbar, ddCtAbsolute, elist, errBarchart, ColMap, replaceVectorByEquality, write.htmltable, writeSimpleTabCsv, DEFAULT.SAMPLE.COLNAME, DEFAULT.FEATURE.COLNAME, DEFAULT.CT.COLNAME, 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: InputReader, SDMReader, TSVReader, QuantStudioReader, ddCtExpression, InputFrame, ColMap Package: ddPCRclust Exports: calculateCPDs, createEnsemble, ddPCRclust, exportPlots, exportToCSV, exportToExcel, readFiles, readTemplate, runDensity, runPeaks, runSam Package: debCAM Exports: AfromMarkers, Amat, CAM, CAMASest, CAMMGCluster, CAMPrep, MDL, MGsforA, MGstatistic, PCAmat, Smat, XWProj, cornerSort, redoASest, reselectMG, sffsHull, simplexplot ExportMethods: plot, PCAmat Package: debrowser Exports: BoxMainPlotControlsUI, IQRPlotControlsUI, actionButtonDE, addDataCols, addID, all2all, all2allControlsUI, applyFilters, applyFiltersNew, applyFiltersToMergedComparison, barMainPlotControlsUI, batchEffectUI, batchMethod, changeClusterOrder, checkCountData, checkMetaData, clustFunParamsUI, clusterData, compareClust, condSelectUI, correctCombat, correctHarman, customColorsUI, cutOffSelectionUI, dataLCFUI, dataLoadUI, deServer, deUI, debrowserIQRplot, debrowserall2all, debrowserbarmainplot, debrowserbatcheffect, debrowserboxmainplot, debrowsercondselect, debrowserdataload, debrowserdeanalysis, debrowserdensityplot, debrowserheatmap, debrowserhistogram, debrowserlowcountfilter, debrowsermainplot, debrowserpcaplot, dendControlsUI, densityPlotControlsUI, distFunParamsUI, drawKEGG, drawPCAExplained, fileTypes, fileUploadBox, generateTestData, getAfterLoadMsg, getAll2AllPlotUI, getBSTableUI, getBarMainPlot, getBarMainPlotUI, getBoxMainPlot, getBoxMainPlotUI, getColorShapeSelection, getColors, getCompSelection, getCondMsg, getConditionSelector, getConditionSelectorFromMeta, getCutOffSelection, getDEAnalysisText, getDEResultsUI, getDataAssesmentText, getDataForTables, getDataPreparationText, getDensityPlot, getDensityPlotUI, getDomains, getDown, getDownloadSection, getEnrichDO, getEnrichGO, getEnrichKEGG, getEntrezIds, getEntrezTable, getGOLeftMenu, getGOPlots, getGeneList, getGeneSetData, getGoPanel, getHeatmapUI, getHelpButton, getHideLegendOnOff, getHistogramUI, getIQRPlot, getIQRPlotUI, getIntroText, getJSLine, getKEGGModal, getLeftMenu, getLegendColors, getLegendRadio, getLegendSelect, getLevelOrder, getLoadingMsg, getLogo, getMainPanel, getMainPlotUI, getMainPlotsLeftMenu, getMean, getMergedComparison, getMetaSelector, getMethodDetails, getMostVariedList, getNormalizedMatrix, getOrganism, getOrganismBox, getOrganismPathway, getPCAPlotUI, getPCAcontolUpdatesJS, getPCAexplained, getPCselection, getPlotArea, getProgramTitle, getQAText, getQCLeftMenu, getQCPanel, getSampleDetails, getSampleNames, getSamples, getSearchData, getSelHeat, getSelectInputBox, getSelectedCols, getSelectedDatasetInput, getShapeColor, getStartPlotsMsg, getStartupMsg, getTabUpdateJS, getTableDetails, getTableModal, getTableStyle, getTextOnOff, getUp, getUpDown, getVariationData, get_conditions_given_selection, heatmapControlsUI, heatmapJScode, heatmapServer, heatmapUI, hideObj, histogramControlsUI, installpack, kmeansControlsUI, lcfMetRadio, loadpack, mainPlotControlsUI, mainScatterNew, niceKmeans, normalizationMethods, palUI, panel.cor, panel.hist, pcaPlotControlsUI, plotData, plotMarginsUI, plotSizeMarginsUI, plotSizeUI, plotTypeUI, plot_pca, prepDEOutput, prepDataContainer, prepGroup, prepHeatData, prepPCADat, push, removeCols, removeExtraCols, round_vals, runDE, runDESeq2, runEdgeR, runHeatmap, runHeatmap2, runLimma, run_pca, selectConditions, selectGroupInfo, selectedInput, sepRadio, setBatch, showObj, startDEBrowser, startHeatmap, textareaInput, togglePanels Package: DECIPHER Exports: Add2DB, Codec, Seqs2DB, SearchDB, DB2Seqs, FormGroups, IdentifyByRank, IdLengths, TerminalChar, DistanceMatrix, IdClusters, MODELS, ReadDendrogram, WriteDendrogram, ConsensusSequence, Disambiguate, IdConsensus, TileSeqs, FindChimeras, CreateChimeras, DesignArray, Array2Matrix, NNLS, CalculateEfficiencyArray, AmplifyDNA, CalculateEfficiencyPCR, DesignPrimers, DesignSignatures, DigestDNA, MeltDNA, CalculateEfficiencyFISH, DesignProbes, BrowseSeqs, BrowseDB, CorrectFrameshifts, OrientNucleotides, PredictDBN, PredictHEC, RemoveGaps, TrimDNA, AdjustAlignment, AlignDB, AlignProfiles, AlignSeqs, AlignTranslation, MaskAlignment, StaggerAlignment, AA_REDUCED, AlignSynteny, FindSynteny, LearnTaxa, IdTaxa Package: deco Exports: decoRDA, decoNSCA, decoReport, AnnotateDECO, plotDECOProfile, plotGainingH, plotHeatmapH, plotAssociationH ExportMethods: NSCAcluster, featureTable, show, summary ExportClasses: deco Package: DEComplexDisease Exports: Plot, bi.deg, cluster.module, deg.specific, module.compare, module.curve, module.extract, module.modeling, module.overlap, module.screen, seed.module, summarize Package: decompTumor2Sig Exports: composeGenomesFromExposures, computeExplainedVariance, convertAlexandrov2Shiraishi, convertGenomesFromVRanges, decomposeTumorGenomes, determineSignatureDistances, downgradeShiraishiSignatures, evaluateDecompositionQuality, getGenomesFromMutFeatData, getSignaturesFromEstParam, isAlexandrovSet, isExposureSet, isShiraishiSet, isSignatureSet, mapSignatureSets, plotDecomposedContribution, plotExplainedVariance, plotMutationDistribution, readAlexandrovSignatures, readGenomesFromMPF, readGenomesFromVCF, readShiraishiSignatures, sameSignatureFormat Package: decontam Exports: isContaminant, isNotContaminant, plot_condition, plot_frequency Package: DeepBlueR Exports: deepblue_aggregate, deepblue_batch_export_results, deepblue_binning, deepblue_cache_status, deepblue_cancel_request, deepblue_chromosomes, deepblue_clear_cache, deepblue_collection_experiments_count, deepblue_commands, deepblue_count_gene_ontology_terms, deepblue_count_regions, deepblue_coverage, deepblue_delete_request_from_cache, deepblue_diff, deepblue_distinct_column_values, deepblue_echo, deepblue_enrich_regions_fast, deepblue_enrich_regions_go_terms, deepblue_enrich_regions_overlap, deepblue_export_bed, deepblue_export_meta_data, deepblue_export_tab, deepblue_extend, deepblue_extract_ids, deepblue_extract_names, deepblue_faceting_experiments, deepblue_filter_regions, deepblue_find_motif, deepblue_flank, deepblue_get_biosource_children, deepblue_get_biosource_parents, deepblue_get_biosource_related, deepblue_get_biosource_synonyms, deepblue_get_experiments_by_query, deepblue_get_regions, deepblue_get_request_data, deepblue_info, deepblue_input_regions, deepblue_intersection, deepblue_is_biosource, deepblue_liftover, deepblue_list_annotations, deepblue_list_biosources, deepblue_list_cached_requests, deepblue_list_column_types, deepblue_list_epigenetic_marks, deepblue_list_experiments, deepblue_list_expressions, deepblue_list_gene_models, deepblue_list_genes, deepblue_list_genomes, deepblue_list_in_use, deepblue_list_projects, deepblue_list_recent_experiments, deepblue_list_requests, deepblue_list_samples, deepblue_list_similar_biosources, deepblue_list_similar_epigenetic_marks, deepblue_list_similar_experiments, deepblue_list_similar_genomes, deepblue_list_similar_projects, deepblue_list_similar_techniques, deepblue_list_techniques, deepblue_merge_queries, deepblue_meta_data_to_table, deepblue_name_to_id, deepblue_options, deepblue_overlap, deepblue_preview_experiment, deepblue_query_cache, deepblue_query_experiment_type, deepblue_reset_options, deepblue_score_matrix, deepblue_search, deepblue_select_annotations, deepblue_select_column, deepblue_select_experiments, deepblue_select_expressions, deepblue_select_genes, deepblue_select_regions, deepblue_tiling_regions ExportMethods: deepblue_download_request_data ExportClasses: DeepBlueCommand Package: deepSNV Exports: RF, bam2R, bbb, betabinLRT, bf2Vcf, dbetabinom, loadAllData, makePrior, manhattanPlot, mcChunk, p.combine, pbetabinom, qvals2Vcf ExportMethods: test, summary, show, repeatMask, p.val, normalize, estimateDispersion, estimateDirichlet, deepSNV, coordinates, control, consensusSequence, [ ExportClasses: deepSNV Package: DEFormats Exports: DGEList, as.DESeqDataSet, as.DGEList, simulateNormFactors, simulateRnaSeqData ExportMethods: DGEList Package: DEGraph Exports: AN.test, BS.test, getConnectedComponentList, getKEGGPathways, getSignedGraph, graph.T2.test, hyper.test, laplacianFromA, plotValuedGraph, randomWAMGraph, testOneConnectedComponent, testOneGraph, twoSampleFromGraph, writeAdjacencyMatrix2KGML Package: DEGreport Exports: DEGSet, as.DEGSet, createReport, deg, degCheckFactors, degColors, degComps, degCorCov, degCovariates, degDefault, degFilter, degMA, degMB, degMDS, degMV, degMean, degObj, degPCA, degPatterns, degPlot, degPlotCluster, degPlotWide, degQC, degResults, degSignature, degSummary, degVB, degVar, degVolcano, geom_cor, significants ExportMethods: significants, degDefault, deg, as.DEGSet Package: DEGseq Exports: DEGexp, DEGexp2, DEGseq, DEGseq, getGeneExp, readGeneExp Package: DelayedArray Exports: aperm.ArbitraryArrayGrid, aperm.RegularArrayGrid, aperm.SparseArraySeed, aperm.DelayedArray, as.array.Array, as.array.SparseArraySeed, as.character.ArrayGrid, as.character.Array, as.complex.Array, as.data.frame.Array, as.integer.Array, as.logical.Array, as.matrix.Array, as.matrix.SparseArraySeed, as.numeric.Array, as.raw.Array, as.vector.Array, mean.DelayedArray, range.DelayedArray, rowsum.DelayedMatrix, split.DelayedArray, summary.DelayedOp, summary.DelayedSubset, summary.DelayedAperm, summary.DelayedUnaryIsoOpStack, summary.DelayedUnaryIsoOpWithArgs, summary.DelayedDimnames, summary.DelayedNaryIsoOp, summary.DelayedAbind, t.Array, unique.DelayedArray, linearInd, ArrayViewport, makeNindexFromArrayViewport, ArbitraryArrayGrid, RegularArrayGrid, SparseArraySeed, dense2sparse, sparse2dense, makeCappedVolumeBox, makeRegularArrayGridOfCappedLengthViewports, setAutoBlockSize, getAutoBlockSize, get_type_size, getAutoBlockLength, setAutoBlockShape, getAutoBlockShape, blockGrid, rowGrid, colGrid, multGrids, showtree, seedApply, modify_seeds, isPristine, contentIsPristine, new_DelayedArray, setAutoGridMaker, getAutoGridMaker, setAutoBPPARAM, getAutoBPPARAM, blockApply, blockReduce, effectiveGrid, currentBlockId, currentViewport, BLOCK_write_to_sink, supportedRealizationBackends, getRealizationBackend, setRealizationBackend, RealizationSink, RleArray, arbind, acbind, extract_array, refdim, maxlength, aperm, downsample, aind, nzdata, sparsity, is_sparse, extract_sparse_array, read_block, write_block, read_sparse_block, write_sparse_block, mapToGrid, mapToRef, isLinear, is_noop, nseed, seed, seed<-, simplify, netSubsetAndAperm, matrixClass, DelayedArray, chunkdim, chunkGrid, close, realize, pmax2, pmin2, apply, rowsum, colsum, rowMaxs, colMaxs, rowMins, colMins, rowRanges, colRanges ExportMethods: arbind, acbind, extract_array, refdim, maxlength, aperm, downsample, aind, nzdata, sparsity, is_sparse, extract_sparse_array, read_block, write_block, mapToGrid, mapToRef, isLinear, is_noop, nseed, seed, seed<-, simplify, netSubsetAndAperm, matrixClass, DelayedArray, chunkdim, chunkGrid, close, realize, pmax2, pmin2, apply, rowsum, colsum, rowMaxs, colMaxs, rowMins, colMins, rowRanges, colRanges, length, names, names<-, dim, dim<-, dimnames, dimnames<-, [, [[, [<-, lengths, as.array, as.matrix, as.data.frame, as.vector, as.logical, as.integer, as.numeric, as.complex, as.character, as.raw, c, split, drop, t, is.na, is.finite, is.infinite, is.nan, !, ==, !=, <=, >=, <, >, sweep, anyNA, which, unique, max, min, range, sum, prod, any, all, mean, round, signif, rowSums, colSums, rowMeans, colMeans, nchar, tolower, toupper, sub, gsub, coerce, show, dnorm, pnorm, qnorm, dbinom, pbinom, qbinom, dpois, ppois, qpois, dlogis, plogis, qlogis, summary, crossprod, tcrossprod, cbind, rbind, dims, grepl, path, path<-, table, type, updateObject, showAsCell, isEmpty, splitAsList, ranges, start, end, width ExportClasses: Array, ArrayViewport, ArrayGrid, ArbitraryArrayGrid, RegularArrayGrid, SparseArraySeed, DelayedOp, DelayedUnaryOp, DelayedSubset, DelayedAperm, DelayedUnaryIsoOp, DelayedUnaryIsoOpStack, DelayedUnaryIsoOpWithArgs, DelayedSubassign, DelayedDimnames, DelayedNaryOp, DelayedNaryIsoOp, DelayedAbind, DelayedArray, DelayedMatrix, DelayedArray1, integer_OR_NULL, RealizationSink, arrayRealizationSink, RleArraySeed, SolidRleArraySeed, RleRealizationSink, ChunkedRleArraySeed, RleArray, RleMatrix Package: DelayedDataFrame Exports: DelayedDataFrame, coerce ExportMethods: replaceCOLS, names, mergeROWS, lazyIndex, extractROWS, extractCOLS, coerce, cbind, as.list, lazyIndex<-, [ ExportClasses: LazyIndex, DelayedDataFrame Package: DelayedMatrixStats Exports: colAlls, colAnyMissings, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse, colCounts, colCummaxs, colCummins, colCumprods, colCumsums, colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs, colMads, colMeans2, colMedians, colOrderStats, colProds, colQuantiles, colRanks, colSdDiffs, colSds, colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads, colWeightedMeans, colWeightedMedians, colWeightedSds, colWeightedVars, rowAlls, rowAnyMissings, rowAnyNAs, rowAnys, rowAvgsPerColSet, rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods, rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps, rowMadDiffs, rowMads, rowMeans2, rowMedians, rowOrderStats, rowProds, rowQuantiles, rowRanks, rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars, rowWeightedMads, rowWeightedMeans, rowWeightedMedians, rowWeightedSds, rowWeightedVars ExportMethods: rowWeightedVars, rowWeightedSds, rowWeightedMedians, rowWeightedMeans, rowWeightedMads, rowVars, rowVarDiffs, rowTabulates, rowSums2, rowSds, rowSdDiffs, rowRanks, rowQuantiles, rowProds, rowOrderStats, rowMedians, rowMeans2, rowMads, rowMadDiffs, rowLogSumExps, rowIQRs, rowIQRDiffs, rowDiffs, rowCumsums, rowCumprods, rowCummins, rowCummaxs, rowCounts, rowCollapse, rowAvgsPerColSet, rowAnys, rowAnyNAs, rowAnyMissings, rowAlls, colWeightedVars, colWeightedSds, colWeightedMedians, colWeightedMeans, colWeightedMads, colVars, colVarDiffs, colTabulates, colSums2, colSds, colSdDiffs, colRanks, colQuantiles, colProds, colOrderStats, colMedians, colMeans2, colMads, colMadDiffs, colLogSumExps, colIQRs, colIQRDiffs, colDiffs, colCumsums, colCumprods, colCummins, colCummaxs, colCounts, colCollapse, colAvgsPerRowSet, colAnys, colAnyNAs, colAnyMissings, colAlls Package: deltaCaptureC Exports: binSummarizedExperiment, downshiftDFtoMatrix, generatePermutation, getDeltaSE, getLopsidedness, getMeanNormalizedCountsSE, getNormalizedCountsSE, getOverlapWeights, getPValueCutoff, getRunAndLopsidednessStatistics, getRunStatisticsDist, getRunTotals, getSignificantRegions, getSizeFactorsDF, getSizeFactorsSE, plotSignificantRegions, rebinToMultiple Package: deltaGseg Exports: parseTraj ExportMethods: chooseBreaks, splitTraj, transformSeries, plotDiff, clusterPV, denoiseSegments, clusterSegments, diagnosticPlots, getAVD, getBreaks, getTNames, getSegments, getTraj, getIntervals, plot, show ExportClasses: SegSeriesTrajectories, SegTrajectories, Trajectories, TransTrajectories Package: DeMAND Exports: runDeMAND, demandClass, printDeMAND Package: DeMixT Exports: DeMixT, DeMixT_S1, DeMixT_S2, Optimum_KernelC Package: DEP Exports: LFQ, TMT, add_rejections, analyze_dep, filter_missval, filter_proteins, get_df_long, get_df_wide, get_prefix, get_results, get_suffix, import_IsobarQuant, import_MaxQuant, impute, make_se, make_se_parse, make_unique, manual_impute, meanSdPlot, normalize_vsn, plot_all, plot_cond, plot_cond_freq, plot_cond_overlap, plot_cor, plot_coverage, plot_detect, plot_dist, plot_frequency, plot_gsea, plot_heatmap, plot_imputation, plot_missval, plot_normalization, plot_numbers, plot_p_hist, plot_pca, plot_single, plot_volcano, process, report, run_app, se2msn, test_diff, test_gsea, theme_DEP1, theme_DEP2 Package: DepecheR Exports: dAllocate, dColorPlot, dColorVector, dContours, dDensityPlot, dResidualPlot, dScale, dSplsda, dViolins, dWilcox, depeche, groupProbPlot Package: DEqMS Exports: spectraCounteBayes, outputResult, VarianceBoxplot, VarianceScatterplot, Residualplot, peptideProfilePlot, medianSummary, medpolishSummary, equalMedianNormalization, medianSweeping, farmsSummary Package: derfinder Exports: advancedArg, analyzeChr, annotateRegions, calculatePvalues, calculateStats, coerceGR, collapseFullCoverage, coverageToExon, createBw, createBwSample, define_cluster, extendedMapSeqlevels, filterData, findRegions, fullCoverage, getRegionCoverage, getTotalMapped, loadCoverage, makeGenomicState, makeModels, mergeResults, preprocessCoverage, railMatrix, rawFiles, regionMatrix, sampleDepth Package: derfinderHelper Exports: fstats.apply Package: derfinderPlot Exports: plotCluster, plotOverview, plotRegionCoverage, vennRegions Package: DEScan2 Exports: RleListToRleMatrix, binnedCoverage, constructBedRanges, countFinalRegions, createGranges, cutGRangesPerChromosome, divideEachSampleByChromosomes, finalRegions, findOverlapsOverSamples, findPeaks, fromSamplesToChrsGRangesList, keepRelevantChrs, readBamAsBed, readBedFile, readFilesAsGRangesList, saveGRangesAsBed, saveGRangesAsTsv, setGRGenomeInfo Package: DESeq Exports: newCountDataSet, estimateVarianceFunctions, varianceFitDiagnostics, residualsEcdfPlot, nbinomTest, getBaseMeansAndVariances, nbinomTestForMatrices, estimateSizeFactorsForMatrix, scvPlot, getVarianceStabilizedData, varianceStabilizingTransformation, makeExampleCountDataSet, adjustScvForBias, fitNbinomGLMsForMatrix, fitNbinomGLMs, nbkd.sf, nbinomGLMTest, dispTable, fitInfo, plotDispEsts, plotMA, plotPCA, newCountDataSetFromHTSeqCount ExportMethods: counts, counts<-, sizeFactors, sizeFactors<-, conditions, conditions<-, dispTable, estimateSizeFactors, estimateDispersions ExportClasses: CountDataSet Package: DESeq2 Exports: dispersionFunction<-, dispersions<-, normalizationFactors<-, priorInfo<-, DESeq, DESeqDataSet, DESeqDataSetFromHTSeqCount, DESeqDataSetFromMatrix, DESeqDataSetFromTximport, DESeqResults, DESeqTransform, collapseReplicates, dispersionFunction, dispersions, estimateBetaPriorVar, estimateDispersionsFit, estimateDispersionsGeneEst, estimateDispersionsMAP, estimateDispersionsPriorVar, estimateMLEForBetaPriorVar, estimateSizeFactorsForMatrix, fpkm, fpm, getVarianceStabilizedData, lfcShrink, makeExampleDESeqDataSet, nbinomLRT, nbinomWaldTest, normTransform, normalizationFactors, normalizeGeneLength, plotCounts, plotSparsity, priorInfo, removeResults, replaceOutliers, replaceOutliersWithTrimmedMean, results, resultsNames, rlog, rlogTransformation, unmix, varianceStabilizingTransformation, vst ExportMethods: summary, sizeFactors, show, priorInfo, plotPCA, plotMA, plotDispEsts, normalizationFactors, estimateSizeFactors, estimateDispersions, dispersions, dispersionFunction, design, counts, sizeFactors<-, priorInfo<-, normalizationFactors<-, dispersions<-, dispersionFunction<-, design<-, counts<- ExportClasses: DESeqTransform, DESeqResults, DESeqDataSet Package: DEsingle Exports: DEsingle, DEtype Package: destiny Exports: dataset<-, distance<-, eigenvalues<-, eigenvectors<-, sigmas<-, DPT, DiffusionMap, DiffusionMapCompat, Sigmas, as.ExpressionSet, branch_divide, colorlegend, cube.helix, cube_helix, dataset, distance, dm.predict, dm_predict, eig.decomp, eig_decomp, eigenvalues, eigenvectors, find.dm.k, find.sigmas, find_dm_k, find_knn, find_sigmas, find_tips, fortify.DPT, fortify.DiffusionMap, gene_relevance, lWhich, l_which, optimal.sigma, optimal_sigma, plot.DPT, plot.DiffusionMap, plot_differential_map, plot_gene_relevance, plot_gradient_map, projection_dist, random_root, read.ExpressionSet, scale_color_cube_helix, scale_colour_cube_helix, scale_fill_cube_helix, sigmas, tips ExportMethods: updateObject, sigmas, show, print, plot_gene_relevance, plot_differential_map, plot, optimal_sigma, nrow, ncol, names, gene_relevance, featureNames, eigenvectors, eigenvalues, distance, dim, dataset, as.matrix, as.data.frame, as.ExpressionSet, sigmas<-, featureNames<-, eigenvectors<-, eigenvalues<-, distance<-, dataset<-, [[, [, $ ExportClasses: Sigmas, GeneRelevance, DiffusionMap, DPT Package: DEsubs Exports: DEsubs, geneVisualization, organismVisualization, subpathwayToGraph, subpathwayVisualization, subpathwayTypes Package: DEWSeq Exports: DESeqDataSetFromSlidingWindows, extractRegions, resultsDEWSeq, toBED, topWindowStats Package: DEXSeq Exports: geneIDs, geneIDs<-, groupIDs, groupIDs<-, exonIDs, exonIDs<-, featureIDs, featureIDs<-, DEXSeqHTML, plotDEXSeq, testForDEU, featureCounts, perGeneQValue, DEXSeqDataSet, DEXSeqDataSetFromSE, DEXSeqDataSetFromHTSeq, DEXSeqResults, estimateExonFoldChanges, DEXSeq, sampleAnnotation ExportMethods: estimateDispersions, plotMA, counts, estimateSizeFactors, subsetByOverlaps, findOverlaps, [, $<-, colData<- ExportClasses: DEXSeqDataSet, DEXSeqResults Package: dexus Exports: conditionSizes, dexss, dexus, dexus.parallel, dispersions, getSizeNB, INICalls, INIThreshold<-, INIThreshold, INIValues, inputData, logFC, means, normalizeData, normalizedData, params, posteriorProbs, pvals, responsibilities, sampleNames, sizeFactors, sizeParameters, transcriptNames ExportMethods: sort, show, plot, INI, as.data.frame, [ ExportClasses: DEXUSResult Package: DFP Exports: discriminantFuzzyPattern, readCSV, plotMembershipFunctions, showDiscreteValues, showFuzzyPatterns, plotDiscriminantFuzzyPattern, calculateMembershipFunctions, discretizeExpressionValues, calculateFuzzyPatterns, calculateDiscriminantFuzzyPattern ExportMethods: show ExportClasses: ExpressionLevel, LowExpressionLevel, MediumExpressionLevel, HighExpressionLevel Package: DiffBind Exports: dba, dba.peakset, dba.overlap, dba.count, dba.contrast, dba.analyze, dba.report, dba.plotHeatmap, dba.plotPCA, dba.plotMA, dba.plotVolcano, dba.plotVenn, dba.plotBox, dba.show, dba.mask, dba.save, dba.load, DBA_GROUP, DBA_ID, DBA_TISSUE, DBA_FACTOR, DBA_CONDITION, DBA_TREATMENT, DBA_CONSENSUS, DBA_CALLER, DBA_CONTROL, DBA_REPLICATE, DBA_INTERVALS, DBA_FRIP, DBA_ALL_ATTRIBUTES, DBA_OLAP_PEAKS, DBA_OLAP_ALL, DBA_OLAP_RATE, DBA_COR, DBA_OLAP, DBA_INALL, DBA_SCORE_RPKM, DBA_SCORE_RPKM_FOLD, DBA_SCORE_READS, DBA_SCORE_READS_FOLD, DBA_SCORE_READS_MINUS, DBA_SCORE_TMM_MINUS_FULL, DBA_SCORE_TMM_MINUS_EFFECTIVE, DBA_SCORE_TMM_READS_FULL, DBA_SCORE_TMM_READS_EFFECTIVE, DBA_SCORE_TMM_MINUS_FULL_CPM, DBA_SCORE_TMM_MINUS_EFFECTIVE_CPM, DBA_SCORE_TMM_READS_FULL_CPM, DBA_SCORE_TMM_READS_EFFECTIVE_CPM, DBA_SCORE_SUMMIT, DBA_SCORE_SUMMIT_ADJ, DBA_SCORE_SUMMIT_POS, DBA_READS_DEFAULT, DBA_READS_BAM, DBA_READS_BED, DBA_EDGER, DBA_EDGER_BLOCK, DBA_EDGER_GLM, DBA_EDGER_CLASSIC, DBA_DESEQ, DBA_DESEQ_BLOCK, DBA_DESEQ_GLM, DBA_DESEQ_CLASSIC, DBA_DESEQ2, DBA_DESEQ2_BLOCK, DBA_ALL_METHODS, DBA_ALL_BLOCK, DBA_ALL_METHODS_BLOCK, DBA_DATA_FRAME, DBA_DATA_RANGEDDATA, DBA_DATA_GRANGES, DBA_DATA_SUMMARIZED_EXPERIMENT, DBA_DATA_DBAOBJECT ExportClasses: DBA Package: diffcoexp Exports: coexpr, comparecor, diffcoexp Package: diffcyt Exports: calcCounts, calcMedians, calcMediansByClusterMarker, calcMediansBySampleMarker, createContrast, createDesignMatrix, createFormula, diffcyt, generateClusters, plotHeatmap, prepareData, testDA_GLMM, testDA_edgeR, testDA_voom, testDS_LMM, testDS_limma, topClusters, topTable, transformData Package: diffGeneAnalysis Exports: assocAnalysis, biasAdjust, curveFit, dataTrim, normalize, refGroup Package: diffHic Exports: diffHicUsersGuide, cutGenome, segmentGenome, emptyGenome, preparePairs, mergePairs, savePairs, prepPseudoPairs, getPairData, prunePairs, loadChromos, loadData, extractPatch, pairParam, readMTX2IntSet, squareCounts, connectCounts, marginCounts, totalCounts, mergeCMs, correctedContact, normalizeCNV, matchMargins, getArea, filterDirect, filterTrended, filterDiag, filterPeaks, enrichedPairs, neighborCounts, boxPairs, clusterPairs, consolidatePairs, diClusters, annotatePairs, compartmentalize, domainDirections, plotPlaid, rotPlaid, plotDI, rotDI, asDGEList, reform ExportClasses: pairParam Package: DiffLogo Exports: ASN, Alphabet, DNA, FULL_ALPHABET, RNA, calculatePvalue, createDiffLogoObject, diffLogo, diffLogoFromPwm, diffLogoTable, diffLogoTableConfiguration, differenceOfICs, drawDiffLogoTable, enrichDiffLogoObjectWithPvalues, enrichDiffLogoTableWithPvalues, extendPwmsFromAlignmentVector, getAlphabetFromCharacters, getAlphabetFromSequences, getPwmFromAlignment, getPwmFromAlignmentFile, getPwmFromFastaFile, getPwmFromFile, getPwmFromHomerFile, getPwmFromPfmOrJasparFile, getPwmFromPwmFile, getSequencesFromAlignmentFile, getSequencesFromFastaFile, informationContent, lossOfAbsICDifferences, multipleLocalPwmsAlignment, normalizePWM, normalizedDifferenceOfProbabilities, prepareDiffLogoTable, probabilities, pwmDivergence, seqLogo, shannonDivergence, sumOfAbsICDifferences, sumOfAbsProbabilityDifferences, sumProbabilities ExportClasses: DiffLogo, Alphabet Package: diffloop Exports: addchr, annotateAnchors, annotateAnchors.bed, annotateAnchors.bigwig, annotateLoops, annotateLoops.dge, bedToGRanges, calcLDSizeFactors, callCCDs, computeBoundaryScores, featureTest, filterLoops, filterSpanningLoops, getHumanGenes, getHumanTSS, getMouseGenes, getMouseTSS, interchromosomal, intrachromosomal, keepCTCFloops, keepEPloops, loopAssoc, loopDistancePlot, loopGenes, loopMetrics, loopPlot, loopWidth, loopsMake, loopsMake.mango, loopsSubset, mangoCorrection, manyLoopPlots, mergeAnchors, numAnchors, numLoops, padGRanges, pcaPlot, plotTopLoops, quickAssoc, quickAssocVoom, removeRegion, removeSelfLoops, rmchr, slidingWindowTest, splitSamples, subsetLoops, subsetRegion, subsetRegionAB, topLoops, updateLDGroups ExportMethods: union, summary, sampleNames, sampleNames<- ExportClasses: loops Package: diffuStats Exports: commuteTimeKernel, diffuse, diffuse_grid, diffuse_mc, diffuse_raw, diffusionKernel, generate_graph, generate_input, inverseCosineKernel, is_kernel, largest_cc, metric_auc, metric_fun, pStepKernel, perf, perf_eval, perf_wilcox, regularisedLaplacianKernel, scores2colours, scores2shapes Package: diggit Exports: aqtl, conditional, correlation, diggitClass, fCNV, marina, mutualInfo ExportMethods: summary, show, print, plot, mindyFiltering, marina, head, fCNV, exprs, diggitViper, diggitRegulon, diggitMindy, diggitMR, diggitFcnv, diggitConditional, diggitCNV, diggitAqtl, conditional, aqtl Package: Director Exports: append2List, createList, drawSankey, filterNumeric, filterRelation, filterSubset, initSankey, makeSankey, writeSankey Package: DirichletMultinomial Exports: dmn, dmngroup, goodnessOfFit, laplace, mixturewt, mixture, heatmapdmn, cvdmngroup, roc, csubset, fitted, predict ExportMethods: AIC, BIC, summary, show ExportClasses: DMN, DMNGroup Package: discordant Exports: createVectors, discordantRun, fishersTrans, splitMADOutlier Package: DiscoRhythm Exports: discoApp, discoBatch, discoCheckInput, discoDFtoSE, discoDesignSummary, discoGetODAs, discoGetSimu, discoInterCorOutliers, discoODAs, discoPCA, discoPCAoutliers, discoParseMeta, discoPeriodDetection, discoRepAnalysis, discoSEtoDF Package: divergence Exports: computeChiSquaredTest, computeMultivariateBinaryMatrix, computeMultivariateDigitization, computeMultivariateSupport, computeQuantileMatrix, computeUnivariateDigitization, computeUnivariateSupport, computeUnivariateTernaryMatrix, findMultivariateGammaWithSupport, findUnivariateGammaWithSupport Package: dks Exports: cred.set, dks, dks.pvalue, pprob.dist, pprob.uniform Package: DMCFB Exports: export.bed ExportMethods: totalReads, readBismark, plotDMCFB, methReads, methLevels, findDMCFB, combine, cBSDMC, totalReads<-, methReads<-, methLevels<- ExportClasses: BSDMC Package: DMCHMM ExportMethods: writeBED, totalReads, readBismark, qqDMCs, methVars, methStates, methReads, methLevels, methHMMCMC, methHMEM, manhattanDMCs, findDMCs, combine, cBSData, cBSDMCs, totalReads<-, methVars<-, methStates<-, methReads<-, methLevels<- ExportClasses: BSData, BSDMCs Package: DMRcaller Exports: analyseReadsInsideRegionsForCondition, computeDMRs, computeDMRsReplicates, computeMethylationDataCoverage, computeMethylationDataSpatialCorrelation, computeMethylationProfile, computeOverlapProfile, filterDMRs, getWholeChromosomes, joinReplicates, mergeDMRsIteratively, plotLocalMethylationProfile, plotMethylationDataCoverage, plotMethylationDataSpatialCorrelation, plotMethylationProfile, plotMethylationProfileFromData, plotOverlapProfile, poolMethylationDatasets, poolTwoMethylationDatasets, readBismark, readBismarkPool, saveBismark Package: DMRcate Exports: dmrcate ExportMethods: cpg.annotate, sequencing.annotate, rmSNPandCH, DMR.plot, extractRanges, changeFDR Package: DMRforPairs Exports: DMRforPairs, merge_classes, regionfinder, testregion, calc_stats, export_data, plot_annotate_region, plot_annotate_gene, plot_annotate_custom_region, plot_annotate_probes, tune_parameters Package: DMRScan Exports: dmrscan, estimateWindowThreshold, makeCpGgenes, makeCpGregions Package: dmrseq Exports: dmrseq, getAnnot, meanDiff, plotDMRs, plotEmpiricalDistribution, simDMRs Package: DNABarcodeCompatibility Exports: distance_filter, experiment_design, file_loading_and_checking, get_all_combinations, get_random_combinations, optimize_combinations Package: DNABarcodes Exports: barcode.set.distances, analyse.barcodes, create.dnabarcodes, create.dnabarcodes.ashlock, demultiplex, create.pool, distance, create.dnabarcodes.clique, create.dnabarcodes.sampling, create.dnabarcodes.conway Package: DNAcopy Exports: CNA, exon.segment, getbdry, segment, segments.p, segments.summary, smooth.CNA, glFrequency, plotSample, zoomIntoRegion Package: DNAshapeR Exports: encodeSeqShape, getFasta, getShape, heatShape, readShape, plotShape, trackShape Package: DominoEffect Exports: align_to_unip, calculate_boundary, DominoEffect, identify_hotspots, import_txdb, map_to_func_elem, GPo_of_hotspots Package: doppelgangR Exports: colFinder, corFinder, doppelgangR, dst, mst.mle, outlierFinder, phenoDist, phenoFinder, pst, qst, rst, smokingGunFinder, st.mle, vectorHammingDist, vectorWeightedDist ExportMethods: summary, show, print, plot ExportClasses: DoppelGang Package: Doscheda Exports: corrPlot, densityPlot, doschedaApp, fitModel, getDatasets, getFinal, getInput, getNorm, getParameters, makeReport, meanSdPlot, pcaPlot, removePeptides, replicatePlot, runDoscheda, runNormalisation, setData, setParameters, volcanoPlot ExportMethods: boxplot ExportClasses: ChemoProtSet Package: DOSE Exports: EXTID2NAME, clusterSim, doSim, enrichDGN, enrichDGNv, enrichDO, enrichNCG, facet_grid, gene2DO, geneID, geneInCategory, geneSim, gseDGN, gseDO, gseNCG, gsfilter, mclusterSim, parse_ratio, setReadable, simplot, theme_dose ExportMethods: summary, show ExportClasses: gseaResult, enrichResult Package: doseR Exports: getLibsizes3, make_RPKM, plotMA.se, dafsFilter, quantFilter, test_diffs, plotRatioBoxes, plotRatioDensity, se.DM, glSeq, generateStats, iqrxFilter, plotExpr, simpleFilter Package: drawProteins Exports: draw_canvas, draw_chains, draw_domains, draw_folding, draw_motif, draw_phospho, draw_recept_dom, draw_regions, draw_repeat, extract_feat_acc, extract_names, extract_transcripts, feature_to_dataframe, get_features, parse_gff, phospho_site_info Package: DRIMSeq Exports: common_precision<-, genewise_precision<-, common_precision, dmDSdata, dmFilter, dmFit, dmPrecision, dmSQTLdata, dmTest, genewise_precision, mean_expression, plotData, plotPValues, plotPrecision, plotProportions, proportions, results, samples ExportMethods: samples, rownames, results, proportions, plotProportions, plotPrecision, plotPValues, plotData, nrow, ncol, names, mean_expression, length, genewise_precision, elementNROWS, dmTest, dmPrecision, dmFit, dmFilter, dim, design, counts, common_precision, colnames, coefficients, rownames<-, names<-, genewise_precision<-, common_precision<-, colnames<-, [[, [, $ Package: DriverNet ExportMethods: actualEvents, drivers, totalEvents ExportClasses: DriverNetResult Package: DropletUtils Exports: barcodeRanks, defaultDrops, downsampleBatches, downsampleMatrix, downsampleReads, emptyDrops, encodeSequences, get10xMolInfoStats, makeCountMatrix, read10xCounts, read10xMolInfo, removeSwappedDrops, swappedDrops, testEmptyDrops, write10xCounts Package: DrugVsDisease Exports: generateprofiles, selectrankedlists, classifyprofile, combineProfiles Package: DSS Exports: newSeqCountSet, estDispersion, estNormFactors, waldTest, DSS.DE, DMLtest, callDML, callDMR, makeBSseqData, showOneDMR, DMLfit.multiFactor, DMLtest.multiFactor ExportMethods: normalizationFactor, normalizationFactor<-, dispersion, dispersion<- ExportClasses: SeqCountSet Package: DTA Exports: tls, DTA.phenomat, DTA.plot.it, DTA.normalize, DTA.map.it, DTA.generate, DTA.estimate, DTA.dynamic.generate, DTA.dynamic.estimate Package: dualKS Exports: dksTrain, dksWeights, dksSelectGenes, dksClassify, dksPerm, KS, dksCustomClass ExportMethods: plot, show, summary ExportClasses: DKSGeneScores, DKSClassifier, DKSPredicted Package: DupChecker Exports: arrayExpressDownload, buildFileTable, geoDownload, validateFile Package: dupRadar Exports: analyzeDuprates, cumulativeDuprateBarplot, duprateExpBoxplot, duprateExpDensPlot, duprateExpFit, duprateExpIdentify, duprateExpPlot, expressionHist, getDupMatStats, getDynamicRange, markDuplicates, readcountExpBoxplot Package: DynDoc Exports: baseVigDesc, editVignetteCode, getPkgVigList, getVigInfo, getVigInfoNames, getVignette, getVignetteCode, getVignetteHeader, hasVigHeaderField, tangleToR, tangleToRFinish, tangleToRRuncode, tangleToRSetup, .transformNames, transformVigInfoLine ExportMethods: chunk<-, chunk, chunkList, chunkName, chunks, codeChunk, codeChunks, evalChunk, evalEnv, getAllCodeChunks, getChunk, getDepends, getKeywords, getOptions, getRequires, getSuggests, indexEntry, numChunks, numOptions, path, pdfPath, setChunk<-, show, summary, SweaveOptions, vigPackage, vigPkgVersion ExportClasses: chunkList, codeChunk, DynDoc, SweaveOptions, Vignette, vignetteCode Package: EasyqpcR Exports: nrmData, calData, totData, badCt, slope Package: easyRNASeq Exports: BamFileList, GRanges, IRanges, SRFilterResult, alignData, basename, chastityFilter, chromosomeFilter, compose, locfit, lp, nFilter, naPositionFilter, newCountDataSet, readAligned ExportMethods: yieldSize, writeGff3, writeFastq, width, validate, unsafeAppend, type, tutorialData, transcriptCounts, stranded, strandProtocol, strand, srFilter, split, simpleRNASeq, seqnames, seqlevels, seqlengths, seqinfo, rowRanges, reduce, readLength, readCoverage, readCounts, ranges, precision, plotNormalizationFactors, plotDispersionEstimates, plotDispLSD, parallelize, paired, organismName, multivariateConditions, metadata, librarySize, getBamFileList, getAnnotation, genomicAnnotation, geneModel, geneCounts, fileName, fetchData, fetchCoverage, featureCounts, exonCounts, estimateSizeFactors, estimateDispersions, easyRNASeq, demultiplex, datasource, createSyntheticTranscripts, countBy, colnames, colData, chrSize, barcodePlot, bamParam, assays, assay, annotParam, RnaSeqParam, RPKM, BamParam, AnnotParam, strand<-, seqnames<-, seqlevels<-, readLength<-, readCoverage<-, readCounts<-, organismName<-, librarySize<-, genomicAnnotation<-, geneModel<-, fileName<-, chrSize<- ExportClasses: RnaSeqParam, RangedSummarizedExperiment, RNAseq, GRanges, BamParam, BamFileList, AnnotParamObject, AnnotParamCharacter, AnnotParam Package: EBarrays Exports: checkCCV, checkModel, checkVarsMar, checkVarsQQ, crit.fun, eb.createFamilyGG, eb.createFamilyLNN, eb.createFamilyLNNMV, ebPatterns, emfit, emfit0, emfit1, emfit2, emfit3, emfitmv, plot.ebarraysEMfit, plotCluster, plotMarginal, postprob Package: EBcoexpress Exports: bwmc, crit.fun, makeMyD, initializeHP, priorDiagnostic, showPair, showNetwork, ebCoexpressFullTCAECM, ebCoexpressOneStep, ebCoexpressZeroStep, ebCoexpressMeta, rankMyGenes Package: EBImage Exports: Image, is.Image, as.Image, Grayscale, Color, colorMode, colorMode<-, imageData, imageData<-, getFrame, getFrames, numberOfFrames, readImage, writeImage, display, displayOutput, renderDisplay, resize, rotate, flip, flop, translate, affine, transpose, thresh, bwlabel, otsu, watershed, propagate, ocontour, paintObjects, rmObjects, reenumerate, colorLabels, filter2, gblur, medianFilter, equalize, clahe, makeBrush, erode, dilate, opening, closing, whiteTopHat, blackTopHat, selfComplementaryTopHat, distmap, floodFill, fillHull, rgbImage, channel, toRGB, colormap, stackObjects, tile, untile, drawCircle, computeFeatures, computeFeatures.basic, computeFeatures.haralick, computeFeatures.moment, computeFeatures.shape, standardExpandRef, gblob, localCurvature ExportMethods: log, Math2, abind, normalize, combine, hist, show, image, Ops, [ ExportClasses: Image Package: EBSeq Exports: crit_fun, DenNHist, EBTest, GetNg, GetPP, MedianNorm, PolyFitPlot, PostFC, QQP, QuantileNorm, RankNorm, EBMultiTest, GetMultiPP, GetPatterns, PlotPattern, GetPPMat, GetMultiFC, PlotPostVsRawFC, GetNormalizedMat, f0, f1, LogN, LogNMulti, GetDEResults Package: EBSeqHMM Exports: EBTest_ext, EBHMMNBfunForMulti, EBHMMNBMultiEM_2chain, EBHMMNBfun, beta.mom, LikefunNBHMM, f0, GetDECalls, GetConfidentCalls, EBSeqHMMTest, GetAllPaths, PlotExp Package: ecolitk Exports: arrowsArc, chromPos2angle, cPlotCircle, ecoli.len, gccontent, linesArc, linesChrom, linesCircle, linkedmultiget, pointsArc, polar2xy, polygonArc, polygonChrom, polygonDisk, rotate, wstringapply, xy2polar Package: EDASeq Exports: newSeqExpressionSet, plotQuality, getGeneLengthAndGCContent ExportMethods: length, width, initialize, barplot, plot, plotQuality, exprs, offst, offst<-, boxplot, meanVarPlot, biasPlot, plotNtFrequency, withinLaneNormalization, betweenLaneNormalization, biasBoxplot, MDPlot, plotRLE, plotPCA, normCounts, normCounts<-, counts, counts<- ExportClasses: SeqExpressionSet Package: EDDA Exports: generateData, testDATs, computeAUC, plotROC, plotPRC Package: edge Exports: fullMatrix<-, fullModel<-, individual<-, nullMatrix<-, nullModel<-, qvalueObj<-, apply_jackstraw, apply_qvalue, apply_snm, apply_sva, betaCoef, build_models, build_study, deSet, fitFull, fitNull, fullMatrix, fullModel, individual, lrt, nullMatrix, odp, qvalueObj, resFull, resNull, show, summary ExportMethods: sType, nullModel, kl_clust, fit_models ExportClasses: deSet, deFit Package: edgeR ExportMethods: show ExportClasses: DGEList, DGEExact, DGEGLM, DGELRT, TopTags Package: eegc Exports: barplotEnrich, categorizeGene, densityPlot, diffGene, dotPercentage, enrichment, functionEnrich, grnPlot, heatmapPlot, markerScatter, networkAnalyze Package: EGAD Exports: assortativity, auc_multifunc, auprc, auroc_analytic, build_binary_network, build_coexp_GEOID, build_coexp_expressionSet, build_coexp_network, build_semantic_similarity_network, build_weighted_network, calculate_multifunc, conv_smoother, extend_network, filter_network, filter_network_cols, filter_network_rows, filter_orthologs, fmeasure, get_auc, get_biogrid, get_counts, get_density, get_expression_data_gemma, get_expression_matrix_from_GEO, get_phenocarta, get_prc, get_roc, make_annotations, make_gene_network, make_genelist, make_transparent, neighbor_voting, node_degree, plot_densities, plot_density_compare, plot_distribution, plot_network_heatmap, plot_prc, plot_roc, plot_roc_overlay, plot_value_compare, predictions, repmat, run_GBA Package: EGSEA Exports: buildCustomIdx, buildGMTIdx, buildGeneSetDBIdx, buildIdx, buildKEGGIdx, buildMSigDBIdx, egsea, egsea.base, egsea.cnt, egsea.combine, egsea.logo, egsea.ma, egsea.ora, egsea.sort, generateReport, getSetByID, getSetByName, getSetScores, getlimmaResults, limmaTopTable, plotBars, plotGOGraph, plotHeatmap, plotMethods, plotPathway, plotSummary, plotSummaryHeatmap, showSetByID, showSetByName, topSets ExportMethods: summary, show, $ ExportClasses: GSCollectionIndex, EGSEAResults Package: eiR Exports: eiInit, eiMakeDb, eiQuery, eiAdd, eiPerformanceTest, eiCluster, setDefaultDistance, addTransform, loadLSHData, freeLSHData Package: eisa Exports: ISA, ISANormalize, ISAIterate, ISAUnique, ISASweep, ISASweepGraph, ISASweepGraphPlot, ISARobustness, ISAFilterRobust, ISAEnrichment, ISAGO, ISAKEGG, ISACHR, ISAmiRNA, gograph, gographPlot, expPlotCreate, expPlotColbar, expPlot, condPlot, overlap, overlapPlot, mnplot, ISAmnplot, ISA2heatmap, profilePlot, ISAHTMLTable, ISAHTMLModules, ISAHTML, annotate ExportMethods: coerce, summary, htmlReport, pvalues, geneCounts, oddsRatios, expectedCounts, universeCounts, universeMappedCount, geneMappedCount, geneIdUniverse, geneIdsByCategory, sigCategories, makeValidParams, ontology, ontology<-, conditional, conditional<-, drive, drive<-, hyperGTest, seedData, runData, getFeatures, getSamples, getFeatureNames, getSampleNames, getFeatureMatrix, getSampleMatrix, getFullFeatureMatrix, getFullSampleMatrix, getFeatureScores, getSampleScores, getNoFeatures, getNoSamples, featureThreshold, sampleThreshold, getOrganism, featExprs, sampExprs, prenormalized, prenormalized<-, hasNA, hasNA<- Package: ELBOW Exports: analyze_elbow, do_elbow_rnaseq, do_elbow, elbow_variance, extract_working_sets, get_elbow_limma, get_pvalue, null_variance, plot_dataset, plot_elbow, replicates_to_fold Package: EMDomics Exports: CVMomics, EMDomics, KSomics, calculate_cvm, calculate_cvm_gene, calculate_emd, calculate_emd_gene, calculate_ks, calculate_ks_gene, plot_cvm_density, plot_cvmnull, plot_cvmperms, plot_emd_density, plot_emdnull, plot_emdperms, plot_ks_density, plot_ksnull, plot_ksperms Package: ENCODExplorer Exports: buildConsensusPeaks, buildExpressionSummary, consensus, createDesign, downloadEncode, file_metadata, files, fuzzySearch, get_encode_df, get_encode_df_demo, get_encode_df_full, metric, metric_data, peaks, queryConsensusPeaks, queryEncode, queryEncodeGeneric, queryExpressionGeneric, queryGeneExpression, queryTranscriptExpression, raw_data, searchEncode, searchToquery, shinyEncode ExportMethods: show, names, metadata, length, names<- ExportClasses: ENCODESummary, ENCODEExpressionSummary, ENCODEBindingConsensus Package: EnhancedVolcano Exports: EnhancedVolcano Package: ENmix Exports: preprocessENmix, bmiq.mc, ComBat.mc, nmode.mc, normalize.quantile.450k, norm.quantile, plotCtrl, QCinfo, QCfilter, pcrplot, freqpoly, multifreqpoly, rm.outlier, rcp, oxBS.MLE, ctrlsva, relic, mpreprocess, getB, B2M, M2B, rgDataSet, methDataSet, dupicc, calc_detP, getCGinfo, getmeth, readidat, readmanifest, estimateCellProp, predSex, methyAge ExportClasses: rgDataSet, methDataSet Package: EnrichedHeatmap Exports: [.normalizedMatrix, print.normalizedMatrix, rbind.normalizedMatrix, EnrichedHeatmap, anno_enriched, as.normalizedMatrix, copyAttr, default_smooth_fun, discretize, dist_by_closeness, enriched_score, extract_anno_enriched, failed_rows, getSignalsFromList, makeWindows, normalizeToMatrix Package: EnrichmentBrowser Exports: comb.ea.results, combResults, compile.grn.from.kegg, compileGRN, config.ebrowser, configEBrowser, de.ana, deAna, download.kegg.pathways, downloadPathways, ea.browse, eaBrowse, ebrowser, exprsHeatmap, get.go.genesets, get.kegg.genesets, getGenesets, ggea.graph, ggea.graph.legend, ggeaGraph, ggeaGraphLegend, gs.ranking, gsRanking, idMap, idTypes, isAvailable, makeExampleData, map.ids, nbea, nbeaMethods, normalize, parse.genesets.from.GMT, pdistr, probe.2.gene.eset, probe2gene, read.eset, readSE, sbea, sbeaMethods, volcano, writeGMT Package: enrichplot Exports: cnetplot, color_palette, dotplot, emapplot, ggtable, ggtitle, goplot, gseadist, gseaplot, gseaplot2, gsearank, heatplot, plot_grid, pmcplot, ridgeplot, upsetplot ExportMethods: upsetplot, ridgeplot, heatplot, gseaplot, goplot, emapplot, dotplot, cnetplot Package: enrichTF Exports: GeneReguPipe, PECA_TF_enrich, findMotifsInRegions, genBackground, geneOntology, regionConnectTargetGene, tfsEnrichInRegions, tissueOpennessConserve, tissueOpennessSpecificity, unzipAndMergeBed ExportMethods: enrichUnzipAndMergeBed, enrichTissueOpennessSpecificity, enrichTissueOpennessConserve, enrichTFsEnrichInRegions, enrichSingleSampleReport, enrichRegionConnectTargetGene, enrichGeneOntology, enrichGenBackground, enrichFindMotifsInRegions ExportClasses: EnrichStep Package: ensembldb Exports: ensDbFromAH, ensDbFromGff, ensDbFromGRanges, ensDbFromGtf, fetchTablesFromEnsembl, listEnsDbs, makeEnsemblSQLiteFromTables, makeEnsembldbPackage, runEnsDbApp, filter, proteinToGenome, proteinToTranscript, genomeToTranscript, transcriptToProtein, genomeToProtein, transcriptToGenome, transcriptToCds, cdsToTranscript, listProteinColumns, EnsDb, EntrezidFilter, ExonidFilter, ExonrankFilter, GeneidFilter, GenebiotypeFilter, SeqnameFilter, SeqstrandFilter, SeqstartFilter, SeqendFilter, TxidFilter, TxbiotypeFilter, UniprotDbFilter, UniprotMappingTypeFilter, OnlyCodingTxFilter, ProtDomIdFilter, ProteinDomainIdFilter, ProteinDomainSourceFilter, TxSupportLevelFilter ExportMethods: seqlevelsStyle, seqlevelsStyle<-, supportedSeqlevelsStyles, seqlevels, columns, keytypes, keys, select, mapIds, hasProteinData, proteins, listUniprotDbs, listUniprotMappingTypes, cdsBy, dbconn, disjointExons, ensemblVersion, exons, exonsBy, exonsByOverlaps, fiveUTRsByTranscript, genes, getGeneRegionTrackForGviz, getGenomeFaFile, getGenomeTwoBitFile, lengthOf, listColumns, listGenebiotypes, listTxbiotypes, listTables, metadata, organism, promoters, returnFilterColumns, returnFilterColumns<-, seqinfo, threeUTRsByTranscript, toSAF, transcripts, transcriptsBy, transcriptsByOverlaps, updateEnsDb, useMySQL, supportedFilters, addFilter, activeFilter, dropFilter, intronsByTranscript, seqnames, show, convertFilter ExportClasses: EnsDb, ProtDomIdFilter, ProteinDomainSourceFilter, UniprotDbFilter, UniprotMappingTypeFilter, OnlyCodingTxFilter, TxSupportLevelFilter Package: ENVISIONQuery Exports: getServices, getServiceNames, getService, getServiceOptions, getToolNames, getTool, getServiceClient, getInputTypes, ENVISIONQuery Package: EpiDISH Exports: CellDMC, epidish, hepidish Package: epigenomix Exports: chipVals, chipVals<-, cpm, ChIPseqSet, acceptanceRate, chains, classification, components, convergence, mmData, listClassificationMethods, weights, bayesMixModel, calculateCrossCorrelation, getAlignmentQuality, integrateData, matchProbeToPromoter, mlMixModel, normalizeChIP, plotChains, plotClassification, plotComponents, summarizeReads ExportMethods: as.data.frame, dim, length, normalize, show, summary ExportClasses: ChIPseqSet, MixModel, MixModelBayes, MixModelML, MixtureComponent Package: epihet Exports: compMatrix, diffHet, epiBox, epiMA, epiMap, epiPCA, epiTSNE, epiNetwork, epiPathway, jaccard, makeGR, moduleAnno, moduleSim, moduleVisual, readGR, splitn, summarize, userobj, shannon Package: epiNEM Exports: AddLogicGates, CreateExtendedAdjacency, CreateRandomGraph, CreateTopology, ExtendTopology, GenerateData, HeatmapOP, Mll, SimEpiNEM, epiAnno, epiNEM, epiScreen Package: epivizr Exports: restartEpiviz, startEpiviz ExportMethods: show ExportClasses: EpivizApp Package: epivizrChart Exports: BlocksTrack, HeatmapPlot, LinePlot, LineTrack, ScatterPlot, StackedBlocksTrack, StackedLinePlot, StackedLineTrack, append_region, epivizChart, epivizEnv, epivizNav, json_parser, json_writer ExportMethods: plot Package: epivizrData Exports: ahToMySQL, createMgr, register ExportMethods: show, as.list, as.data.frame ExportClasses: EpivizMeasurement, EpivizDataMgr, EpivizData Package: epivizrServer Exports: createServer, json_writer ExportClasses: EpivizServer Package: epivizrStandalone Exports: setStandalone, startStandalone, startStandaloneApp Package: erccdashboard Exports: annotLODR, dynRangePlot, erccROC, estLODR, est_r_m, geneExprTest, initDat, maSignal, runDashboard, saveERCCPlots Package: erma Exports: genemodel, makeErmaSet, stateProfile, stateProf, mapmeta, cellTypes, geneTxRange, csProfile, map2range, subsetByRanges ExportClasses: ErmaSet Package: ERSSA Exports: comb_gen, count_filter, erssa, erssa_deseq2, erssa_deseq2_parallel, erssa_edger, erssa_edger_parallel, ggplot2_TPR_FPRPlot, ggplot2_dotplot, ggplot2_intersectPlot, ggplot2_marginPlot Package: esATAC Exports: atacPipe, atacPipe2, atacRepsPipe, atacRepsPipe2, atacUnzipAndMerge, bam2bed, bamsort, bedToBigWig, bedUtils, bowtie2Mapping, cutsitecount, extractcutsite, fragLenDistr, fripQC, getAllConfigure, getConfigure, getMotifInfo, goanalysis, libComplexQC, motifscan, motifscanpair, peakCalling, peakQC, peakanno, peakcomp, printMap, qcreport, removeAdapter, renamer, sam2bam, samToBed, setConfigure, snpanno, tssQC, unzipAndMerge ExportMethods: process, isSingleEnd, isReady, getReportVal, getReportItems, getProcName, getParamItems, getParam, clearProcCache, atacpeakComp, atacTSSQC, atacSamToBed, atacSam2Bam, atacSNPAnno, atacRenamer, atacRemoveAdapter, atacQCReport, atacPrintMap, atacPeakQC, atacPeakCalling, atacPeakAnno, atacMotifScanPair, atacMotifScan, atacLibComplexQC, atacGOAnalysis, atacFripQC, atacFragLenDistr, atacExtractCutSite, atacCutSiteCount, atacBowtie2Mapping, atacBedUtils, atacBedToBigWig, atacBamSort, atacBam2Bed ExportClasses: ATACProc Package: esetVis Exports: esetLda, esetPlotWrapper, esetSpectralMap, esetTsne, getGeneSetsForPlot, plotEset ExportClasses: rbokehEsetPlot, ggvisEsetPlot, ggplotEsetPlot, esetPlotInteractive, esetPlot Package: eudysbiome Exports: Cartesian, assignTax, contingencyCount, contingencyTest, microAnnotate, tableSpecies Package: evaluomeR Exports: stability, stabilityRange, quality, qualityRange, metricsCorrelations, getDataQualityRange Package: EventPointer Exports: CDFfromGTF, CDFfromGTF_Multipath, EventDetection, EventDetectionMultipath, EventPointer, EventPointer_IGV, EventPointer_RNASeq, EventPointer_RNASeq_IGV, EventPointer_RNASeq_TranRef, EventsGTFfromTrancriptomeGTF, FindPrimers, GetPSI_FromTranRef, PSI_Statistic, PrepareBam_EP, getbootstrapkallisto Package: ExCluster Exports: GFF_convert, processCounts, ExCluster, plotExonlog2FC, GRangesFromExClustResults Package: ExiMiR Exports: ReadExi, createAB, NormiR, bg.correct.miR, norm.miR, summarize.miR, NormiR.bgcorrect.methods, NormiR.normalize.methods, NormiR.pmcorrect.methods, NormiR.summary.methods, NormiR.spikein.args, make.gal.env Package: exomeCopy Exports: subdivideGRanges, countBamInGRanges, getGCcontent, generateBackground, exomeCopy, copyCountSegments, plot.ExomeCopy, compileCopyCountSegments, plotCompiledCNV, negLogLike, viterbiPath ExportMethods: show, plot ExportClasses: ExomeCopy Package: ExperimentHub Exports: ExperimentHub, getExperimentHubOption, setExperimentHubOption, createHubAccessors ExportMethods: cache, [[, listResources, loadResources, package ExportClasses: ExperimentHub Package: ExperimentHubData Exports: ExperimentHubMetadata, makeExperimentHubMetadata, addResources ExportClasses: ExperimentHubMetadata Package: ExpressionAtlas Exports: getAtlasExperiment, getAtlasData, searchAtlasExperiments Package: ExpressionView Exports: LaunchEV ExportMethods: ExportEV, OrderEV Package: fabia Exports: fabia, fabias, fabiap, spfabia, readSamplesSpfabia, samplesPerFeature, readSpfabiaResult, mfsc, fabiasp, fabi, projFunc, projFuncPos, estimateMode, nmfsc, nmfeu, nmfdiv, matrixImagePlot, plotBicluster, extractPlot, extractBic, makeFabiaData, makeFabiaDataBlocks, makeFabiaDataPos, makeFabiaDataBlocksPos, fabiaDemo, fabiaVersion ExportMethods: plot, summary, show, showSelected, parameters, n, p1, p2, l, center, scaleData, X, L, Z, M, LZ, U, avini, xavini, ini, Psi, lapla, parameters<-, n<-, p1<-, p2<-, l<-, center<-, scaleData<-, X<-, L<-, Z<-, M<-, LZ<-, U<-, avini<-, xavini<-, ini<-, Psi<-, lapla<- ExportClasses: Factorization Package: factDesign Exports: contrastTest, findFC, kRepsOverA, madOutPair, outlierPair, par2lambda Package: FamAgg Exports: FAData, connectedSubgraph, doPlotPed, estimateTimeAtRisk, factor2matrix, ped2graph, sliceAge, subPedigree, switchPlotfun, binomialTest ExportMethods: familialIncidenceRate, familialIncidenceRateTest, fsir, fsirTest, genealogicalIndexTest, kinshipSumTest, kinshipGroupTest, probabilityTest, runSimulation, getAll, getExternalMatched, getGenerationMatched, getGenerationSexMatched, getSexMatched, countGenerations, estimateGenerations, generationsFrom, getAncestors, getChildren, getSiblings, getMissingMate, getCommonAncestor, findFounders, getFounders, getSingletons, $, [, affectedIndividuals, affectedKinshipGroups, age, age<-, buildPed, cliques, cliques<-, cliqueAndTrait, export, family, kinship, lambda, pedigree, pedigree<-, pedigreeSize, phenotypedIndividuals, removeSingletons, plotPed, plotRes, resultForId, shareKinship, result, trait, trait<-, traitByClique, timeAtRisk, timeAtRisk<-, timeInStrata ExportClasses: FAData, FAProbResults, FAKinGroupResults, FAKinSumResults, FAGenIndexResults, FAIncidenceRateResults, FAStdIncidenceRateResults, FABinTestResults Package: farms Exports: expFarms, qFarms, lFarms, generateExprVal.method.farms ExportMethods: summary, plot, INIcalls, getI_Eset, getNI_Eset, getI_ProbeSets, getNI_ProbeSets ExportClasses: INI_Calls Package: fastLiquidAssociation Exports: fastMLA, mass.CNM, fastboots.GLA ExportMethods: fastMLA, mass.CNM, fastboots.GLA ExportClasses: fastMLA, mass.CNM, fastboots.GLA Package: FastqCleaner Exports: adapter_filter, check_encoding, complex_filter, fixed_filter, inject_letter_random, launch_fqc, length_filter, n_filter, qmean_filter, random_length, random_qual, random_seq, seq_filter, seq_names, trim3q_filter, unique_filter Package: fastseg Exports: fastseg, segPlot, toDNAcopyObj Package: FCBF Exports: IG, SU, discretize_exprs, discretize_exprs_supervised, discretize_gene_supervised, fcbf, get_ig, get_su, su_plot Package: fCCAC Exports: fccac Package: fCI ExportMethods: call.npci, compute, figures, normalization, populate, summarize, venndiagram, find.fci.targets ExportClasses: NPCI Package: fcoex Exports: discretize, find_cbf_modules, get_nets, idents, mod_colors, mod_gene_num, mod_names, mod_ora, module_genes, new_fcoex, nmodules, ora_data, plot_interactions, plot_ora, recluster, save_plots, show_net, show_ora ExportMethods: show 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: FELLA Exports: addGOToGraph, buildDataFromGraph, buildGraphFromKEGGREST, defineCompounds, enrich, exportResults, generateEnzymesTable, generateResultsGraph, generateResultsTable, getBackground, getCom, getExcluded, getGraph, getInfo, getInput, getName, getPscores, is.FELLA.DATA, is.FELLA.USER, launchApp, listApprox, listCategories, listInternalDatabases, listMethods, loadKEGGdata, plotGraph, runDiffusion, runHypergeom, runPagerank ExportMethods: show, plot ExportClasses: FELLA.USER, FELLA.DATA Package: ffpe Exports: CATplot ExportMethods: sampleQC, sortedIqrPlot Package: FGNet Exports: FGNet_GUI, FGNet_report, fea_gtLinker, fea_gtLinker_getResults, fea_david, fea_gage, fea_topGO, format_david, format_results, readGeneTermSets, fea2incidMat, functionalNetwork, clustersDistance, analyzeNetwork, getTerms, plotGoAncestors, keywordsTerm, plotKegg Package: fgsea Exports: calcGseaStat, collapsePathways, fgsea, fgseaLabel, fgseaMultilevel, gmtPathways, multilevelError, plotEnrichment, plotGseaTable, reactomePathways Package: FindMyFriends Exports: defaults<-, geneNames<-, groupInfo<-, groupNames<-, orgInfo<-, orgNames<-, .fillDefaults, .loadPgExample, addGenomes, addGroupInfo, addOrgInfo, cdhitGrouping, collapseParalogues, defaults, geneLocation, geneNames, geneWidth, genes, getNeighborhood, getRep, gpcGrouping, graphGrouping, groupGenes, groupInfo, groupNames, groupStat, hasGeneGroups, hasGeneInfo, hasParalogueLinks, kmerLink, kmerSimilarity, kmerSplit, manualGrouping, mergePangenomes, nGeneGroups, nGenes, nOrganisms, neighborhoodSplit, orgInfo, orgNames, orgStat, pangenome, pcGraph, pgMatrix, plotEvolution, plotGroup, plotNeighborhood, plotSimilarity, plotStat, plotTree, readAnnot, removeGene, reportGroupChanges, seqToGeneGroup, seqToOrg, setGroupInfo, setOrgInfo, translated, variableRegions ExportClasses: pgVirtualLoc, pgVirtual, pgSlimLoc, pgSlim, pgLMLoc, pgLM, pgInMemLoc, pgInMem, pgFullLoc, pgFull Package: FISHalyseR Exports: calculateMaxEntropy, calculateThreshold, analyseParticles, computeIlluminationCorrection, processFISH Package: fishpond Exports: computeInfRV, deswish, labelKeep, makeSimSwishData, plotInfReps, plotMASwish, readEDS, scaleInfReps, swish Package: FitHiC Exports: FitHiC Package: flagme ExportMethods: show, plot ExportClasses: peaksDataset Package: flowAI Exports: flow_auto_qc, flow_iQC Package: flowBeads Exports: BeadFlowFrame, mefTransform ExportMethods: toMEF, relativeNormalise, plot, length, hasMEF, getTransformFunction, getParams, getMEFtransform, getMEFparams, getDate, getClusteringStats, generateReport, gateBeads, absoluteNormalise ExportClasses: GatedBeadFlowFrame, BeadFlowFrame Package: flowBin Exports: checkQNorm, flowBin ExportMethods: tube.set, tube.set<-, show, removeSparseBins, quantileNormalise, name, name<-, measure.pars, measure.pars<-, mapBinsKNN, kMeansBin, getBinExpr, flowFPBin, eventsInBins, control.tubes, control.tubes<-, checkQNorm, bin.pars, bin.pars<-, bin.labels, bin.labels<- ExportClasses: FlowSample, BinnedFlowSample Package: flowcatchR Exports: Frames, add.contours, channel.Frames, crop.Frames, export.Frames, export.particles, inspect.Frames, kinematics, link.particles, matchTrajToParticles, normalizeFrames, particles, penaltyFunctionGenerator, plot2D.TrajectorySet, preprocess.Frames, read.Frames, read.particles, rotate.Frames, select.Frames, select.particles, shinyFlow, snap, trajectories ExportMethods: show ExportClasses: TrajectorySet, ParticleSet, LinkedParticleSet, KinematicsFeaturesSet, KinematicsFeatures, Frames Package: flowCHIC Exports: fcs_to_img, img_sub, calculate_overlaps_xor, plot_nmds ExportMethods: fcs_to_img, img_sub, calculate_overlaps_xor, plot_nmds Package: flowCL Exports: flowCL, test.flowCL.connection Package: flowClean Exports: clean Package: flowClust Exports: criterion<-, ruleOutliers<-, Map, SimulateMixture, box, criterion, density, dmvt, dmvtmix, flowClust, flowClust2Prior, getEstimates, importance, mkPrior, peakMatch, plot, plotPrior, posterior, rbox, ruleOutliers, split, summary, tmixFilter, uncertainty ExportMethods: summarizeFilter, show, plot, mkPrior, length, density, Subset, [[, [, %in% ExportClasses: tmixFilterResultList, tmixFilterResult, tmixFilter, flowDens, flowClustList, flowClust Package: flowCore Exports: %&%, %in%, %on%, %subset%, colnames<-, filterDetails<-, identifier<-, keyword<-, markernames<-, parameters<-, Data, EHtrans, FCSTransTransform, Subset, action, actions, alias, arcsinhTransform, asinht, asinhtGml2, assign, biexponentialTransform, boundaryFilter, char2ExpressionFilter, cleanup, collapse_desc, compensate, compensatedParameter, compensation, decompensate, dg1polynomial, each_col, each_row, ellipsoidGate, estimateLogicle, estimateMedianLogicle, exponential, expressionFilter, filter, filterDetails, filterList, filterReference, filter_keywords, filters, filtersList, flowFrame, flowSet, fr_append_cols, fsApply, gate, getChannelMarker, getIndexSort, head, hyperlog, hyperlogtGml2, identifier, inverseLogicleTransform, invsplitscale, isFCSfile, isNull, journal, keyword, kmeansFilter, linearTransform, lintGml2, lnTransform, logTransform, logarithm, logicleTransform, logicletGml2, logtGml2, ls, manyFilterResult, markernames, normalization, normalize, parameters, parent, polygonGate, polytopeGate, print, quadGate, quadratic, quadraticTransform, ratio, ratiotGml2, read.FCS, read.FCSheader, read.flowSet, rectangleGate, rotate_gate, sampleFilter, scaleTransform, scale_gate, shift_gate, sinht, spillover, spillover_match, split, splitScaleTransform, splitscale, squareroot, summarizeFilter, tail, timeFilter, transform, transformList, transformReference, transform_gate, tree, truncateTransform, unitytransform, views, write.FCS, write.flowSet ExportMethods: varMetadata, varLabels, transform, toTable, tail, summary, summarizeFilter, split, spillover, show, sampleNames, rbind2, range, print, plot, phenoData, parameters, pData, nrow, normalize, ncol, names, markernames, length, keyword, initialize, identifier, head, getIndexSort, fsApply, filterReference, filterDetails, filter, featureNames, exprs, eval, each_row, each_col, dim, description, decompensate, compensate, colnames, cbind2, c, Subset, |, varMetadata<-, varLabels<-, sampleNames<-, phenoData<-, pData<-, markernames<-, identifier<-, filterDetails<-, exprs<-, description<-, colnames<-, [[, [, >=, >, ==, <=, <, *, &, %subset%, %on%, %in%, %&%, $, ! ExportClasses: unitytransform, unionFilter, transformReference, transformMap, transformList, transformFilter, transform, timeFilter, subsetFilter, squareroot, splitscale, sinht, setOperationFilter, sampleFilter, rectangleGate, ratiotGml2, ratio, randomFilterResult, quadratic, quadGate, polytopeGate, polygonGate, parameters, parameterTransform, parameterFilter, normalization, manyFilterResult, logtGml2, logicletGml2, logicalFilterResult, logarithm, lintGml2, kmeansFilter, invsplitscale, intersectFilter, hyperlogtGml2, hyperlog, flowSet, flowFrame, filtersList, filters, filterSummaryList, filterSummary, filterResultList, filterResult, filterReference, filterList, filter, expressionFilter, exponential, ellipsoidGate, dg1polynomial, concreteFilter, complementFilter, compensation, compensatedParameter, boundaryFilter, asinhtGml2, asinht, EHtrans Package: flowCyBar Exports: normalize, cybar_plot, nmds, correlation ExportMethods: normalize, cybar_plot, nmds, correlation Package: flowDensity Exports: flowDensity, plot, getflowFrame, deGate, plotDens, getPeaks, notSubFrame, nmRemove, .trackSlope ExportClasses: CellPopulation Package: flowFit Exports: parentFitting, logTicks, proliferationGrid, generationsDistance, proliferationFitting, proliferationIndex, getGenerations ExportMethods: initialize, show, summary, Data, confint, coef, plot ExportClasses: parentFittingData, proliferationFittingData Package: flowFP Exports: flowFPModel, is.flowFPModel, flowFP, is.flowFP, flowFPPlex, is.flowFPPlex ExportMethods: show, summary, name, tags, sampleNames, sampleClasses, sampleClasses<-, hasClasses, counts, nFeatures, nInstances, binBoundary, nRecursions, nRecursions<-, length, length<-, parameters, plot, append, [, [[ ExportClasses: flowFPModel, flowFP, flowFPPlex Package: flowMap Exports: getFR, getFRest, getFRmat, makeDistmat, makeFRMST, statCrossLists ExportClasses: FRstats Package: flowMatch Exports: Cluster, ClusteredSample, mahalanobis.dist, symmetric.KL, dist.cluster, dist.matrix, dist.sample, dist.template, match.clusters, match.clusters.dist, create.template, template.tree, MetaCluster, Template ExportMethods: plot, summary, get.size, get.dimension, get.center, get.cov, get.cluster.id, get.sample.id, get.num.clusters, get.clusters, get.labels, get.num.metaclusters, get.template.id, get.metaClusters, get.tree, get.match12, get.match21, get.matching.cost, get.unmatch.penalty, sample.id<- ExportClasses: Cluster, ClusteredSample, ClusterMatch, MetaCluster, Template Package: flowMeans Exports: flowMeans, changepointDetection, plot, summary, show Package: flowMerge Exports: fitPiecewiseLinreg, pFlowMerge, checkForRemoteErrors, flowObj, ENT, NENT, BIC, ICL, split, map, ptree ExportMethods: getData, merge, plot, summary, show, split ExportClasses: flowMerge, flowObj Package: flowPeaks Exports: flowPeaks, adjust.flowPeaks, assign.flowPeaks, evalCluster Package: flowPloidy Exports: FlowHist, batchFlowHist, browseFlowHist, fhAnalyze, fhAnnotation, fhArgs, fhBins, fhCV, fhChannel, fhComps, fhCounts, fhDebris, fhFail, fhFile, fhG2, fhGate, fhHistData, fhInit, fhLimits, fhLinearity, fhModel, fhNLS, fhOpts, fhPeaks, fhRCS, fhRaw, fhSamples, fhSpecialParams, fhStandards, fhStdPeak, fhStdSelected, fhStdSizes, pickInit, plotFH, setBins, stdPeak, stdSelected, stdSizes, tabulateFlowHist, updateFlowHist, viewFlowChannels 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: FlowRepositoryR Exports: flowRep.ls, flowRep.get, flowRep.search, flowRep.submitImpcResults, flowRep.submitGeneStatus, getFlowRepositoryURL, setFlowRepositoryURL, setFlowRepositoryCredentials, forgetFlowRepositoryCredentials, fcs.files<-, attachments<-, impcCodeDescription, ilarCodeDescription, listKnownIlarCodes, flowRepData, fcsProxy, attachmentProxy, flowRepOrganization ExportMethods: summary, is.downloaded, download, id, fcs.files, attachments, fcs.files<-, attachments<-, localpath, organizations, impcResultsCopy, impc.experiments, impc.experiments<- ExportClasses: flowRepData, fcsProxy, attachmentProxy, flowRepOrganization Package: FlowSOM Exports: AggregateFlowFrames, BuildMST, BuildSOM, CountGroups, FMeasure, FlowSOM, FlowSOMSubset, GetCVs, GetClusters, GetFlowJoLabels, GetMFIs, GetMetaclusters, Initialize_KWSP, Initialize_PCA, MetaClustering, MetaclusterCVs, MetaclusterMFIs, NewData, PlotCenters, PlotClusters2D, PlotGroups, PlotLabels, PlotMarker, PlotNode, PlotNumbers, PlotOverview2D, PlotPies, PlotSD, PlotStars, PlotVariable, Purity, QueryStarPlot, ReadInput, SOM, SaveClustersToFCS, TestOutliers, UpdateNodeSize, get_channels, get_markers, metaClustering_consensus Package: flowSpecs Exports: arcTrans, corrMatCreate, correctUnmix, flowSet2LongDf, oneVsAllPlot, specMatCalc, specUnmix Package: flowSpy Exports: %in%, Rphenograph, buildTree, constraintMatrix, correctBatchFSPY, createFSPY, defLeafCells, defRootCells, fetchCell, fetchClustMeta, fetchPlotMeta, find_neighbors, gatingMatrix, plot2D, plot3D, plotBranchHeatmap, plotCluster, plotClusterHeatmap, plotHeatmap, plotMarkerDensity, plotPieCluster, plotPieTree, plotPseudotimeDensity, plotPseudotimeTraj, plotTrajHeatmap, plotTree, plotViolin, processingCluster, runClara, runCluster, runDiff, runDiffusionMap, runExprsExtract, runExprsMerge, runFastPCA, runHclust, runKNN, runKmeans, runMclust, runPhenograph, runPseudotime, runSOM, runTSNE, runUMAP, runWalk, subsetFSPY, updateClustMeta, updatePlotMeta ExportMethods: show ExportClasses: FSPY Package: flowStats Exports: lymphGate, norm2Filter, curv1Filter, curv2Filter, curvPeaks, oneDGate, quadrantGate, rangeGate, rangeFilter, warpSet, proBin, binByRef, gaussNorm, plotBins, calcPearsonChi, calcPBChiSquare, gpaSet, iProcrustes, normQA, singletGate, overton_like, gate_singlet, spillover_ng ExportMethods: %in%, normalize, spillover, spillover_match, spillover_ng ExportClasses: lymphFilter, rangeFilter, curv1Filter, curv2Filter, norm2Filter Package: flowTime Exports: addbs, addnorm, annotateFlowSet, createAnnotation, flsummary, getTime, loadGates, ploidy, polyGate, qaGating, read.plateSet, saveGates, steadyState, summarizeFlow Package: flowTrans Exports: flowTrans, extractParams, summary.flowTransResult ExportMethods: flowTrans Package: flowType Exports: flowType, decodePhenotype, plot, summary, getLabels, encodePhenotype, calcNumPops, calcMemUse ExportClasses: Phenotypes Package: flowUtils Exports: read.gatingML, testGatingMLCompliance, write.gatingML Package: flowViz Exports: flowViz.par.get, flowViz.par.set, panel.densityplot.flowset.stack, panel.ecdfplot.flowset, panel.xyplot.flowframe, panel.xyplot.flowframe.time, panel.xyplot.flowset, prepanel.densityplot.flowset.stack, prepanel.ecdfplot.flowset, prepanel.xyplot.flowframe, prepanel.xyplot.flowframe.time, prepanel.xyplot.flowset, timelineplot ExportMethods: xyplot, timeLinePlot, splom, qqmath, plot, parallel, levelplot, histogram, gpolygon, gpoints, glpolygon, glpoints, glines, flowPlot, ecdfplot, densityplot, contour, addName Package: flowVS Exports: transFlowVS, estParamFlowVS, lymphs, microVS, plotMeanSd Package: flowWorkspace Exports: flowData<-, gs_cyto_data<-, .getNodeInd, GatingSetList, Rm, add, asinh_Gml2, asinhtGml2_trans, booleanFilter, char2booleanFilter, checkRedundantNodes, clone, compute_timestep, copyNode, dropRedundantChannels, dropRedundantNodes, extract_cluster_pop_name_from_node, filterObject, filter_to_list, fix_channel_slash, flowData, flowJo.fasinh, flowJo.flog, flowJo.fsinh, flowJoTrans, flowJo_biexp_trans, flowJo_fasinh_trans, flowWorkspace.par.get, flowWorkspace.par.set, flow_breaks, flow_trans, flowjo_biexp, flowjo_biexp_trans, flowjo_fasinh, flowjo_fasinh_trans, flowjo_fsinh, flowjo_log_trans, getChildren, getCompensationMatrices, getData, getDescendants, getGate, getNodes, getParent, getPopStats, getProp, getSingleCellExpression, getSingleCellExpressionByGate, getStats, getTotal, getTransformations, get_leaf_nodes, get_log_level, gh_apply_to_new_fcs, gh_copy_gate, gh_get_cluster_labels, gh_get_compensations, gh_get_leaf_nodes, gh_get_pop_paths, gh_get_transformations, gh_plot_pop_count_cv, gh_pop_compare_stats, gh_pop_get_children, gh_pop_get_cluster_name, gh_pop_get_count, gh_pop_get_data, gh_pop_get_descendants, gh_pop_get_full_path, gh_pop_get_gate, gh_pop_get_indices, gh_pop_get_indices_mat, gh_pop_get_parent, gh_pop_get_proportion, gh_pop_get_stats, gh_pop_get_stats_tfilter, gh_pop_is_bool_gate, gh_pop_is_gated, gh_pop_is_hidden, gh_pop_is_negated, gh_pop_move, gh_pop_remove, gh_pop_set_gate, gh_pop_set_indices, gh_pop_set_name, gh_pop_set_visibility, gh_pop_set_xml_count, groupByChannels, groupByTree, gs_check_redundant_nodes, gs_clone, gs_cyto_data, gs_get_compensation_internal, gs_get_leaf_nodes, gs_get_pop_paths, gs_get_singlecell_expression, gs_get_singlecell_expression_by_gate, gs_is_h5, gs_plot_diff_tree, gs_plot_pop_count_cv, gs_pop_add, gs_pop_get_children, gs_pop_get_count_fast, gs_pop_get_count_with_meta, gs_pop_get_data, gs_pop_get_gate, gs_pop_get_parent, gs_pop_get_stats, gs_pop_get_stats_tfilter, gs_pop_remove, gs_pop_set_gate, gs_pop_set_name, gs_pop_set_visibility, gs_remove_redundant_channels, gs_remove_redundant_nodes, gs_split_by_channels, gs_split_by_tree, gs_update_channels, gslist_to_gs, isGated, isHidden, isNcdf, isNegated, load_gs, load_gslist, logicleGml2_trans, logicle_trans, logtGml2_trans, mkformula, moveNode, openWorkspace, plotGate, pop.MFI, pop_add, prettyAxis, save_gs, save_gslist, setGate, setNode, set_log_level, swap_data_cols, transformerList, updateChannels ExportMethods: updateIndices, transform, show, setNode, setGate, sampleNames, recompute, rbind2, plotGate, plot, pData, markernames, length, lapply, keyword, identifier, gs_cyto_data, getPopStats, getParent, getNodes, getIndices, getGate, getData, getChildren, flowData, compensate, colnames, clone, GatingSet, sampleNames<-, pData<-, markernames<-, identifier<-, gs_cyto_data<-, flowData<-, colnames<-, [[<-, [[, [ ExportClasses: booleanFilter, GatingSetList, GatingSet, GatingHierarchy Package: fmcsR Exports: fmcs, fmcsBatch, plotMCS, mcs2sdfset ExportMethods: stats, mcs1, mcs2, [[, coerce, show ExportClasses: MCS Package: focalCall Exports: focalCall, FreqPlot, FreqPlotfocal, igvFiles, singleSample ExportClasses: cghCall Package: FoldGO Exports: FoldSpecTest, FuncAnnotGroupsTopGO, GAFReader, GeneGroups, getAnnotation, getFStable, getGroups, getIntNames, getNFStable, getQuanNumber, getRegType, getResultList, getResultTable, getVersion, getWholeIntName ExportMethods: plot, getWholeIntName, getVersion, getResultTable, getResultList, getRegType, getQuanNumber, getNFStable, getIntNames, getGroups, getFStable, getAnnotation Package: FourCSeq Exports: FourC, addFragments, addPeaks, addViewpointFrags, combineFragEnds, countFragmentOverlaps, countFragmentOverlapsSecondCutter, distFitMonotone, distFitMonotoneSymmetric, findViewpointFragments, getAllResults, getDifferences, getDistAroundVp, getNormalizationFactors, getReferenceSeq, getZScores, normalizeRPM, plotDifferences, plotFits, plotNormalizationFactors, plotScatter, plotZScores, smoothCounts, smoothHitPerCent, writeTrackFiles ExportMethods: updateObject ExportClasses: FourC Package: frma Exports: frma, barcode, GNUSE ExportMethods: initialize, se.exprs, weights, residuals, randomeffects, se.exprs<-, weights<-, residuals<-, randomeffects<- ExportClasses: frmaExpressionSet Package: frmaTools Exports: makeVectorsAffyBatch, makeVectorsFeatureSet, makeVectorPackage, convertPlatform Package: FunChIP Exports: summit_peak, choose_k, cluster_peak, pileup_peak, distance_peak, plot_peak, smooth_peak, compute_fragments_length, silhouette_plot, bending_index ExportMethods: summit_peak, choose_k, cluster_peak, pileup_peak, plot_peak, smooth_peak Package: FunciSNP Exports: getFSNPs, FunciSNPAnnotateSummary, FunciSNPplot, FunciSNPbed, FunciSNPtable, FunciSNPsummaryOverlaps, FunciSNPidsFromSummary, alt.allele<-, alt.allele, chr<-, chr, correlated.snps<-, correlated.snps, yafsnp.dprime<-, yafsnp.dprime, genotype<-, genotype, pop.genotype, pop.genotype<-, overlapping.features<-, overlapping.features, population<-, population, position<-, position, ref.allele<-, ref.allele, yafsnp.rsq<-, yafsnp.rsq, yafsnp.pvalue, yafsnp.pvalue<-, snpid<-, snpid ExportMethods: alt.allele<-, alt.allele, chr<-, chr, correlated.snps<-, correlated.snps, yafsnp.dprime<-, yafsnp.dprime, genotype<-, genotype, pop.genotype, pop.genotype<-, overlapping.features<-, overlapping.features, population<-, population, position<-, position, ref.allele<-, ref.allele, yafsnp.rsq<-, yafsnp.rsq, yafsnp.pvalue, yafsnp.pvalue<-, snpid<-, snpid ExportClasses: CorrelatedSNPs, TagSNP, TSList Package: funtooNorm Exports: agreement, fromGenStudFiles, fromRGChannelSet, funtooNorm, getGRanges, getNormBeta, getNormM, getRawBeta, getSnpM, plotValidationGraph ExportMethods: show ExportClasses: SampleSet Package: GA4GHclient Exports: HGVSnames, getBiosample, getCallSet, getDataset, getExpressionLevel, getFeature, getFeatureSet, getIndividual, getReadGroupSet, getReference, getReferenceSet, getRnaQuantification, getRnaQuantificationSet, getVariant, getVariantAnnotationSet, getVariantSet, listReferenceBases, makeVCFFromGA4GHResponse, makeVCFHeaderFromGA4GHResponse, searchBiosamples, searchCallSets, searchDatasets, searchExpressionLevels, searchFeatureSets, searchFeatures, searchIndividuals, searchPhenotypeAssociationSets, searchPhenotypeAssociations, searchReadGroupSets, searchReads, searchReferenceSets, searchReferences, searchRnaQuantificationSets, searchRnaQuantifications, searchVariantAnnotationSets, searchVariantAnnotations, searchVariantSets, searchVariants, searchVariantsByGRanges Package: GA4GHshiny Exports: app, countGenotype Package: gaga Exports: adjustfitNN, checkfit, classpred, dcgamma, findgenes, fitGG, fitNN, fitNNSingleHyp, forwsimDiffExpr, geneclus, getpar, mcgamma, parest, posmeansGG, powfindgenes, rcgamma, simGG, simLNN, simNN, simnewsamples, powclasspred, seqBoundariesGrid, buildPatterns, plotForwSim Package: gage Exports: eg2sym, sym2eg, essGene, esset.grp, gage, gagePrep, gageSum, gageComp, gagePipe, geneData, gs.tTest, gs.zTest, gs.KSTest, heter.gage, pairData, go.gsets, kegg.gsets, readExpData, readList, sigGeneSet Package: gaggle Exports: gaggleInit, getNameList, getCluster, getMatrix, getNetwork, getTuple, broadcast, geese, getTargetGoose, setTargetGoose, setSpecies, getSpecies, showGoose, hideGoose, testGagglePackage, connectToGaggle, disconnectFromGaggle, getJavaClassName, getTupleAsList, tupleToList, newSingle, addSingle, newTuple Package: gaia Exports: runGAIA, load_cnv, load_markers Package: GAPGOM Exports: expression_prediction, expression_semantic_scoring, fantom_download, fantom_load_raw, fantom_to_expset, set_go_data, topo_ic_sim_genes, topo_ic_sim_term Package: GAprediction Exports: predictGA, extractSites Package: GARS Exports: GARS_create_rnd_population, GARS_FitFun, GARS_Elitism, GARS_Selection, GARS_Crossover, GARS_Mutation, GARS_PlotFitnessEvolution, GARS_PlotFeaturesUsage, GARS_GA ExportMethods: FitScore, AllPop, LastPop, MatrixFeatures ExportClasses: GarsSelectedFeatures Package: GateFinder Exports: GateFinder, plot.GateFinder ExportMethods: plot ExportClasses: GatingProjection Package: gcapc Exports: bindWidth, gcEffects, gcapcPeaks, peaksCAT, read5endCoverage, refinePeaks, refineSites Package: gcatest Exports: gcat, gcat.stat, gcatest Package: gCMAP Exports: annotate_eset_list, center_eSet, eSetOnDisk, generate_gCMAP_NChannelSet, eset_instances, go2cmap, KEGG2cmap, mapNmerge, memorize, mergeCMAPs, reactome2cmap, signedRankSumTest, splitPerturbations, wiki2cmap, zScores ExportMethods: camera_score, CMAPCollection, cmapTable, connectivity_score, downIds, docs, docs<-, effect, effect<-, errors, errors<-, featureScores, fisher_score, gsealm_score, gsealm_jg_score, geneIds, geneIndex, geneScores, geneSign, geneSign<-, incidence, induceCMAPCollection, initialize, labels, labels<-, mapIdentifiers, mergeCollections, members, mgsa_score, minSetSize, plot, padj, padj<-, pval, pval<-, mroast_score, romer_score, set, set<-, setSizes, show, signed, signed<-, SignedGeneSet, nFound, nFound<-, trend, trend<-, upIds, nSet, nSet<-, wilcox_score, zscores ExportClasses: SignedGeneSet, CMAPCollection, CMAPResults Package: gCMAPWeb Exports: exampleCMAP, examplePost, gCMAPWeb, load_cmaps, validate_config_file Package: gCrisprTools Exports: ct.DirectionalTests, ct.GCbias, ct.PRC, ct.PantherPathwayEnrichment, ct.ROC, ct.RRAaPvals, ct.RRAalpha, ct.RRAalphaBatch, ct.alignmentChart, ct.alphaBeta, ct.applyAlpha, ct.ecdf, ct.filterReads, ct.gRNARankByReplicate, ct.generateResults, ct.guideCDF, ct.inputCheck, ct.makeContrastReport, ct.makeQCReport, ct.makeReport, ct.makeRhoNull, ct.normalizeBySlope, ct.normalizeGuides, ct.normalizeMedians, ct.normalizeNTC, ct.normalizeSpline, ct.prepareAnnotation, ct.preprocessFit, ct.rawCountDensities, ct.resultCheck, ct.stackGuides, ct.targetSetEnrichment, ct.topTargets, ct.viewControls, ct.viewGuides 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: GCSscore Exports: GCSscore, get3primeIVTprobefileData, getWTgeneexonprobefileData, getClariomSprobefileData, getXTAprobefileData Package: GDCRNATools Exports: gdcBarPlot, gdcCEAnalysis, gdcClinicalDownload, gdcClinicalMerge, gdcCorPlot, gdcDEAnalysis, gdcDEReport, gdcEnrichAnalysis, gdcEnrichPlot, gdcExportNetwork, gdcFilterDuplicate, gdcFilterSampleType, gdcHeatmap, gdcKMPlot, gdcMatchSamples, gdcParseMetadata, gdcRNADownload, gdcRNAMerge, gdcSurvivalAnalysis, gdcVolcanoPlot, gdcVoomNormalization, shinyCorPlot, shinyKMPlot, shinyPathview Package: GDSArray Exports: GDSArray, GDSFile, example ExportMethods: seed, gdsnodes, gdsfile, extract_array, dimnames, dim, coerce, seed<-, gdsfile<-, $ ExportClasses: GDSMatrix, GDSFile, GDSArray Package: gdsfmt Exports: add.gdsn, addfile.gdsn, addfolder.gdsn, append.gdsn, apply.gdsn, assign.gdsn, cache.gdsn, cleanup.gds, closefn.gds, clusterApply.gdsn, cnt.gdsn, compression.gdsn, copyto.gdsn, createfn.gds, delete.attr.gdsn, delete.gdsn, diagnosis.gds, digest.gdsn, get.attr.gdsn, getfile.gdsn, getfolder.gdsn, index.gdsn, is.element.gdsn, lasterr.gds, ls.gdsn, moveto.gdsn, name.gdsn, objdesp.gdsn, openfn.gds, permdim.gdsn, print.gds.class, print.gdsn.class, put.attr.gdsn, read.gdsn, readex.gdsn, readmode.gdsn, rename.gdsn, setdim.gdsn, showfile.gds, summarize.gdsn, sync.gds, system.gds, write.gdsn, unload.gdsn ExportMethods: show Package: geecc Exports: runConCub, filterConCub, plotConCub, GO2list, KEGG2list, GO2level, GO2offspring, pval2star, intersectPresort, setdiffPresort, sortAscii, p.value, p.value<-, minimum.l2or, minimum.l2or<-, test.direction, test.direction<-, skip.zeroobs, skip.zeroobs<-, skip.min.obs, skip.min.obs<-, skip.min.group, skip.min.group<-, drop.insignif.layer, drop.insignif.layer<-, drop.wrongdir.layer, drop.wrongdir.layer<-, drop.lowl2or.layer, drop.lowl2or.layer<- ExportMethods: show, initialize, getTable ExportClasses: concub, concubfilter Package: GEM Exports: GEM_Emodel, GEM_GUI, GEM_GWASmodel, GEM_Gmodel, GEM_GxEmodel Package: gemini Exports: %<>%, %>%, gemini_boxplot, gemini_calculate_lfc, gemini_create_input, gemini_inference, gemini_initialize, gemini_plot_mae, gemini_prepare_input, gemini_score, initialize_s, initialize_tau, initialize_x, initialize_y, update_mae, update_s_pb, update_tau_pb, update_x_pb, update_y_pb 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: genbankr Exports: GBAccession, GenBankFile, accession, definition, locus, makeTxDbFromGenBank, make_gbrecord, otherFeatures, parseGenBank, readGenBank, sources, variants, vers ExportMethods: vers, variants, transcripts, sources, seqinfo, otherFeatures, makeTxDbFromGenBank, locus, isCircular, intergenic, import, getSeq, genes, exonsBy, exons, definition, cdsBy, cds, accession ExportClasses: GenBankRecord, GenBankFile, GBKFile, GBAccession Package: GeneAccord Exports: GeneAccord, build_null_test_statistic, compute_rates_clon_excl, compute_test_stat_avg_rate, convert_ensembl_to_reactome_pw_tbl, create_ensembl_gene_tbl_hg, create_tbl_ent_clones, create_tbl_tree_collection, ecdf_lr_test_clon_excl_avg_rate, ensembl_to_hgnc, ensembl_to_reactome, extract_num_clones_tbl, generate_ecdf_test_stat, generate_test_stat_hist, get_hist_clon_excl, get_hist_clon_excl_this_pat_this_pair, get_rate_diff_branch_ent_pair, heatmap_clones_gene_pat, hgnc_to_ensembl, is_diff_branch_ent_pair, map_pairs_to_hgnc_symbols, merge_clones_identical_ents, pairs_in_patients_hist, plot_ecdf_test_stat, plot_rates_clon_excl, take_pairs_and_get_patients, vis_pval_distr_num_pat, write_res_pairs_to_disk Package: GeneAnswers Exports: categoryNet, chartPlots, drawTable, geneAnnotationHeatmap, geneAnswersBuilder, geneAnswersChartPlots, geneAnswersConceptNet, geneAnswersConcepts, geneAnswersHeatmap, geneAnswersHomoMapping, geneAnswersReadable, geneAnswersSort, geneConceptNet, getCategoryList, getCategoryTerms, getConceptTable, getDOLiteTerms, getGOList, getHomoGeneIDs, getPATHList, getPATHTerms, getSymbols, groupReport, getListGIF, searchEntrez, topCategory, topCategoryGenes, topDOLITE, topDOLITEGenes, topGO, topGOGenes, topPATH, topPATHGenes, topREACTOME.PATH, topREACTOME.PATHGenes, topcaBIO.PATH, topcaBIO.PATHGenes, geneAnswersConceptRelation, getConnectedGraph, getMultiLayerGraphIDs, getSingleLayerGraphIDs, getNextGOIDs, buildNet, getTotalGeneNumber, getREACTOMEPATHList, getREACTOMEPATHTerms, getcaBIOPATHList, getcaBIOPATHTerms, entrez2caBIO, caBIO2entrez ExportMethods: getGeneInput, getTestType, getPValueT, getGenesInCategory, getGeneExprProfile, getAnnLib, getCategoryType, getEnrichmentInfo, setGeneInput, setTestType, setPValueT, setGeneExprProfile, setAnnLib, setCategoryType, setGenesInCategory, setEnrichmentInfo ExportClasses: GeneAnswers Package: geneAttribution Exports: geneModels, loadBed, normP, geneAttribution Package: GeneBreak Exports: getBreakpoints, bpFilter, addGeneAnnotation, bpGenes, bpStats, recurrentGenes, bpPlot, accessOptions, callData, segmentData, breakpointData, featureChromosomes, geneChromosomes, featureInfo, geneInfo, featuresPerGene, breakpointsPerGene, sampleNames, namesFeatures Package: geneClassifiers Exports: getBatchCorrection, getCitations, getClassifications, getClassifier, getDecisionBoundaries, getDescription, getEventChain, getIntercept, getMeans, getName, getNormalizationMethod, getNormalizationMethods, getProbeNames, getScores, getSds, getTargetValue, getTrainingData, getWeightingType, getWeightingTypes, getWeights, runClassifier, setNormalizationMethod, showClassifierList ExportMethods: runClassifier, getWeights, getWeightingType, getTrainingData, getTargetValue, getSds, getScores, getProbeNames, getNormalizationMethod, getName, getMeans, getIntercept, getEventChain, getDescription, getDecisionBoundaries, getClassifier, getClassifications, getCitations, getBatchCorrection, dim, [[, [ Package: GeneExpressionSignature Exports: getRLs, RankMerging, ScorePGSEA, ScoreGSEA, SignatureDistance Package: genefilter Exports: Anova, coxfilter, cv, eSetFilter, varFilter, featureFilter, fastT, ttest, shorth, half.range.mode, rowttests, colttests, rowFtests, colFtests, rowSds, rowVars, dist2, filterfun, findLargest, gapFilter, genefilter, genescale, getFilterNames, getFuncDesc, getRdAsText, isESet, kOverA, maxA, pOverA, parseArgs, parseDesc, setESetArgs, showESet, kappa_t, kappa_p, filtered_p, filtered_R, rejection_plot, filter_volcano ExportMethods: genefinder, show, plot, [, sens, spec, area, pAUC, AUC, rowpAUCs, nsFilter ExportClasses: rowROC Package: GeneGA Exports: GeneGA, GeneFoldGA, GeneCodon ExportMethods: show, plotGeneGA ExportClasses: GeneGA, GeneFoldGA Package: GeneGeneInteR Exports: CCA.test, CLD.test, GBIGM.test, GGI, importFile, KCCA.test, PCA.test, PLSPM.test, gates.test, imputeSnpMatrix, minP.test, selectSnps, snpMatrixScour, tProd.test, tTS.test Package: GeneMeta Exports: CountPlot, dstar, f.Q, IDRplot, multExpFDR, mu.tau2, sigmad, tau2.DL, var.tau2, zScoreFDR, zScorePermuted, zScores ExportMethods: getdF Package: GeneNetworkBuilder Exports: browseNetwork, browseNetworkOutput, buildNetwork, convertID, exportNetwork, filterNetwork, networkFromGenes, polishNetwork, renderBrowseNetwork, uniqueExprsData Package: GeneOverlap Exports: newGeneOverlap, newGOM ExportMethods: show, print, getListA, setListA<-, getListB, setListB<-, getIntersection, getUnion, getGenomeSize, setGenomeSize<-, getTested, getContbl, getPval, getOddsRatio, getJaccard, testGeneOverlap, getGsetA, getGsetB, getSelfCompare, getMatrix, getNestedList, [, drawHeatmap ExportClasses: GeneOverlap, GeneOverlapMatrix Package: geneplast Exports: gplast.preprocess, groot.preprocess, groot.plot, ogr2tni, ogr2igraph ExportMethods: gplast, gplast.get, groot, groot.get ExportClasses: OGP, OGR Package: geneplotter Exports: alongChrom, cColor, cPlot, cScale, dChip.colors, greenred.colors, GetColor, plotChr, plotExpressionGraph, make.chromOrd, savepng, savepdf, saveeps, savetiff, histStack, groupedHeatmap, openHtmlPage, closeHtmlPage, multiecdf, multidensity ExportMethods: imageMap, Makesense, plotMA Package: geneRecommender Exports: gr.cv, gr.main, gr.normalize Package: GeneRegionScan Exports: exonStructure, findSequenceInGenome, getMetaprobesetsFromRegionOfInterest, getLocalMetaprobeIntensities, findProbePositions, getServerProbeIntensities, getLocalProbeIntensities, getProbesetsFromRegionOfInterest, getProbesetsFromMetaprobeset ExportMethods: getSequence, translateSampleNames, plotOnGene, excludeDoubleMatchingProbes, addSnpPdata, geneRegionScan, plotCoexpression ExportClasses: ProbeLevelSet Package: geneRxCluster Exports: critVal.alpha, critVal.power, critVal.target, gRxCluster, gRxPlot, gRxPlotClumps, gRxSummary, noprune, prune.loglik Package: GeneSelectMMD Exports: gsMMD, gsMMD.default, gsMMD2, gsMMD2.default, errRates, plotHistDensity, obtainResi Package: GENESIS Exports: admixMapMM, assocTestMM, fitNullMM, fitNullReg, king2mat, pcrelateMakeGRM, pcrelateReadInbreed, pcrelateReadKinship, admixMap, calcISAFBeta, correctKin, correctK0, correctK2, kin2gds, mat2gds, nullModelInvNorm, pcairPartition, pcrelateSampBlock, samplesGdsOrder, varCompCI ExportMethods: assocTestSingle, assocTestAggregate, fitNullModel, kingToMatrix, makeSparseMatrix, pcair, pcrelate, pcrelateToMatrix Package: GeneStructureTools Exports: DEXSeqIdsToGeneIds, UTR2UTR53, addBroadTypes, addIntronInTranscript, alternativeIntronUsage, annotateGeneModel, attrChangeAltSpliced, exonsToTranscripts, filterGtfOverlap, filterWhippetEvents, findDEXexonType, findExonContainingTranscripts, findIntronContainingTranscripts, findJunctionPairs, formatWhippetEvents, getOrfs, getUOrfs, leafcutterTranscriptChangeSummary, makeGeneModel, maxLocation, orfDiff, orfSimilarity, overlapTypes, readWhippetDIFFfiles, readWhippetDataSet, readWhippetJNCfiles, readWhippetPSIfiles, removeDuplicateTranscripts, removeSameExon, removeVersion, reorderExonNumbers, replaceJunction, skipExonInTranscript, summariseExonTypes, transcriptChangeSummary, whippetTranscriptChangeSummary ExportMethods: readCounts, junctions, diffSplicingResults, coordinates ExportClasses: whippetDataSet 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: geneXtendeR Exports: allPeakLengths, annotate, annotate_n, barChart, cumlinePlot, diffGO, distinct, gene_annotate, gene_lookup, hotspotPlot, linePlot, makeNetwork, makeWordCloud, meanPeakLength, meanPeakLengthPlot, peakLengthBoxplot, peaksInput, peaksMerge, plotWordFreq Package: GENIE3 Exports: GENIE3, getLinkList ExportMethods: GENIE3 Package: genoCN Exports: code.genotype, genoCNA, genoCNV, plotCN Package: GenoGAM Exports: getChunkSize<-, getOverhangSize<-, getTileNumber<-, getTileSize<-, GenoGAM, GenoGAMDataSet, GenoGAMSettings, callPeaks, computeRegionSignificance, computeSignificance, computeSizeFactors, dataRange, fits, genogam, getChromosomes, getChunkSize, getCoefs, getCountMatrix, getFamily, getIndex, getKnots, getOverhangSize, getParams, getSettings, getTileNumber, getTileSize, is.HDF5, makeTestGenoGAM, makeTestGenoGAMDataSet, makeTestGenoGAMDataSetList, makeTestGenoGAMList, plotGenoGAM, pvalue, readData, se, tileSettings, writeToBEDFile ExportClasses: GenoGAMSettings, GenoGAMDataSet, GenoGAM Package: genomation Exports: heatMatrix, heatMeta, intersectScoreMatrixList, multiHeatMatrix, plotMeta, plotGeneAnnotation, heatTargetAnnotation, plotTargetAnnotation, readGeneric, readBed, readBroadPeak, readNarrowPeak, listSliceMean, listSliceMedian, listSliceMax, listSliceMin, listSliceSum, Mean_c, Median_c, Max_c, Min_c, Sum_c, gffToGRanges, ScoreMatrixList ExportMethods: scaleScoreMatrixList, scaleScoreMatrix, ScoreMatrixBin, ScoreMatrix, readTranscriptFeatures, readFeatureFlank, randomizeFeature, orderBy, patternMatrix, getTargetAnnotationStats, getRandomEnrichment, getMembers, getFlanks, getFeatsWithTargetsStats, getAssociationWithTSS, findFeatureComb, enrichmentMatrix, convertBed2Introns, convertBed2Exons, convertBedDf, binMatrix, annotateWithGeneParts, annotateWithFeatureFlank, annotateWithFeatures, annotateWithFeature ExportClasses: ScoreMatrixList, ScoreMatrix, RandomEnrichment, AnnotationByGeneParts, AnnotationByFeature Package: GenomeInfoDb Exports: orderSeqlevels, rankSeqlevels, fetchExtendedChromInfoFromUCSC, mapGenomeBuilds, genomeBuilds, listOrganisms, genomeStyles, extractSeqlevels, extractSeqlevelsByGroup, mapSeqlevels, seqlevelsInGroup, keepSeqlevels, dropSeqlevels, renameSeqlevels, restoreSeqlevels, standardChromosomes, keepStandardChromosomes, Seqinfo, checkCompatibleSeqinfo, GenomeDescription, summary.Seqinfo, loadTaxonomyDb, available.species, seqinfo, seqinfo<-, seqnames, seqnames<-, seqlevels, seqlevels<-, sortSeqlevels, seqlevelsInUse, seqlevels0, seqlengths, seqlengths<-, isCircular, isCircular<-, genome, genome<-, seqlevelsStyle, seqlevelsStyle<-, commonName, provider, providerVersion, releaseDate, releaseName, bsgenomeName ExportMethods: seqinfo, seqnames, seqnames<-, seqlevels, seqlevels<-, sortSeqlevels, seqlevelsInUse, seqlengths, seqlengths<-, isCircular, isCircular<-, genome, genome<-, seqlevelsStyle, seqlevelsStyle<-, commonName, provider, providerVersion, releaseDate, releaseName, bsgenomeName, length, names, names<-, [, as.data.frame, show, merge, summary, intersect, organism, species ExportClasses: Seqinfo, GenomeDescription Package: genomeIntervals Exports: GenomeIntervals, getGffAttribute, parseGffAttributes ExportMethods: xtfrm, writeGff3, width, which_nearest, strand, sort, size, show, seqnames, seq_name, readZeroLengthFeaturesGff3, readGff3, readBasePairFeaturesGff3, rank, interval_union, interval_overlap, interval_intersection, interval_complement, inter_base, distance_to_nearest, core_annotated, coerce, c, annotation, type<-, strand<-, seqnames<-, seq_name<-, inter_base<-, annotation<-, [[, [, $ ExportClasses: Genome_intervals_stranded, Genome_intervals Package: GenomicAlignments Exports: as.data.frame.OverlapEncodings, levels.OverlapEncodings, validCigar, CIGAR_OPS, explodeCigarOps, explodeCigarOpLengths, cigarToRleList, cigarRangesAlongReferenceSpace, cigarRangesAlongQuerySpace, cigarRangesAlongPairwiseSpace, extractAlignmentRangesOnReference, cigarWidthAlongReferenceSpace, cigarWidthAlongQuerySpace, cigarWidthAlongPairwiseSpace, cigarNarrow, cigarQNarrow, cigarOpTable, queryLoc2refLoc, queryLocs2refLocs, GAlignments, GAlignmentPairs, GAlignmentsList, GappedReads, Lencoding, Rencoding, Lnjunc, Rnjunc, findMateAlignment, makeGAlignmentPairs, getDumpedAlignments, countDumpedAlignments, flushDumpedAlignments, readGAlignments, readGAlignmentPairs, readGAlignmentsList, readGappedReads, NATURAL_INTRON_MOTIFS, summarizeJunctions, readTopHatJunctions, readSTARJunctions, sequenceLayer, pileLettersAt, stackStringsFromGAlignments, stackStringsFromBam, alphabetFrequencyFromBam, encodeOverlaps1, flipQuery, selectEncodingWithCompatibleStrand, extractQueryStartInTranscript, countCompatibleOverlaps, Union, IntersectionNotEmpty, IntersectionStrict, rname, rname<-, cigar, qwidth, njunc, last, strandMode, strandMode<-, isProperPair, qseq, Loffset, Roffset, flippedQuery, encodingHalves, isCompatibleWithSplicing, readGAlignments, readGAlignmentPairs, readGAlignmentsList, readGappedReads, junctions, qnarrow, encodeOverlaps, isCompatibleWithSkippedExons, extractSteppedExonRanks, extractSpannedExonRanks, extractSkippedExonRanks, findCompatibleOverlaps, summarizeOverlaps, findSpliceOverlaps, mapToAlignments, pmapToAlignments, mapFromAlignments, pmapFromAlignments ExportMethods: rname, rname<-, cigar, qwidth, njunc, first, last, strandMode, strandMode<-, isProperPair, qseq, Loffset, Roffset, flippedQuery, encodingHalves, isCompatibleWithSplicing, readGAlignments, readGAlignmentPairs, readGAlignmentsList, readGappedReads, junctions, qnarrow, encodeOverlaps, isCompatibleWithSkippedExons, extractSteppedExonRanks, extractSpannedExonRanks, extractSkippedExonRanks, findCompatibleOverlaps, summarizeOverlaps, findSpliceOverlaps, mapToAlignments, pmapToAlignments, mapFromAlignments, pmapFromAlignments, length, names, names<-, c, [[, show, coerce, unlist, order, sort, rank, levels, update, as.data.frame, is.unsorted, start, end, width, strand, strand<-, invertStrand, updateObject, bindROWS, getListElement, parallelSlotNames, elementMetadata<-, pcompare, ranges, rglist, relistToClass, findOverlaps, windows, narrow, coverage, pintersect, seqinfo, seqinfo<-, seqnames, seqnames<-, seqlevelsInUse, granges, grglist, encoding, second ExportClasses: GAlignments, GAlignmentPairs, GAlignmentsList, GappedReads, OverlapEncodings Package: GenomicDataCommons Exports: aggregations, annotations, available_expand, available_fields, available_rnaseq_workflows, available_values, cases, count, default_fields, endpoints, entity_name, expand, facet, files, filter, gdc_cache, gdc_client, gdc_clinical, gdc_rnaseq, gdc_set_cache, gdc_token, gdcdata, get_facets, get_filter, grep_fields, id_field, ids, make_filter, manifest, mapping, parameters, projects, query, readDNAcopy, readHTSeqFile, response, response_all, results, results_all, select, slicing, status, transfer, transfer_help, write_manifest Package: GenomicFeatures Exports: DEFAULT_CIRC_SEQS, makeTxDb, supportedUCSCtables, browseUCSCtrack, getChromInfoFromUCSC, makeTxDbFromUCSC, getChromInfoFromBiomart, makeTxDbFromBiomart, makeTxDbFromEnsembl, makeTxDbFromGRanges, makeTxDbFromGFF, supportedUCSCFeatureDbTracks, supportedUCSCFeatureDbTables, UCSCFeatureDbTableSchema, makeFeatureDbFromUCSC, id2name, transcripts, exons, cds, genes, transcriptsBy, exonsBy, cdsBy, intronsByTranscript, fiveUTRsByTranscript, threeUTRsByTranscript, transcriptsByOverlaps, exonsByOverlaps, cdsByOverlaps, transcriptLengths, tidyTranscripts, tidyExons, tidyIntrons, exonicParts, intronicParts, disjointExons, features, microRNAs, tRNAs, extractTranscriptSeqs, extractUpstreamSeqs, getPromoterSeq, makePackageName, makeTxDbPackage, makeTxDbPackageFromUCSC, makeTxDbPackageFromBiomart, makeFDbPackageFromUCSC, supportedMiRBaseBuildValues, mapToTranscripts, pmapToTranscripts, mapFromTranscripts, pmapFromTranscripts, transcriptLocs2refLocs, transcriptWidths, mapToTranscripts, pmapToTranscripts, mapFromTranscripts, pmapFromTranscripts, coverageByTranscript, pcoverageByTranscript ExportMethods: species, organism, show, as.list, seqlevels0, seqlevels<-, seqinfo, transcripts, exons, cds, genes, promoters, transcriptsByOverlaps, exonsByOverlaps, cdsByOverlaps, transcriptsBy, exonsBy, cdsBy, intronsByTranscript, fiveUTRsByTranscript, threeUTRsByTranscript, disjointExons, microRNAs, tRNAs, extractTranscriptSeqs, extractUpstreamSeqs, getPromoterSeq, isActiveSeq, isActiveSeq<-, asBED, asGFF, distance, mapToTranscripts, pmapToTranscripts, mapFromTranscripts, pmapFromTranscripts, mapIdsToRanges, mapRangesToIds ExportClasses: TxDb, FeatureDb Package: GenomicFiles Exports: GenomicFiles, files, files<-, reduceByFile, reduceByRange, pack, unpack, rownames, colnames, .fileTypeRegistry, registerFileType, findTypeRegistry, makeFileType, reduceFiles, reduceRanges, reduceByYield, REDUCEsampler, VcfStack, RangedVcfStack, readVcfStack, getVCFPath, paths1kg ExportMethods: GenomicFiles, files, files<-, reduceByFile, reduceByRange, pack, unpack, rownames, colnames, [, dim, names, show, yieldSize, colData<-, countBam, scanBam, summarizeOverlaps, coverage, summary, seqinfo, seqinfo<-, rowRanges, rowRanges<-, assay, colData, vcfFields ExportClasses: GenomicFiles, VcfStack, RangedVcfStack Package: GenomicInteractions Exports: interactionCounts<-, name<-, GenomicInteractions, InteractionTrack, anchorOne, anchorTwo, annotateInteractions, annotateRegions, annotationFeatures, availableDisplayPars, calculateDistances, categoriseInteractions, countsBetweenAnchors, export.bed12, export.bedpe, export.chiasig, export.igraph, get_binom_ligation_threshold, get_self_ligation_threshold, interactionCounts, is.cis, is.dd, is.dt, is.pd, is.pp, is.pt, is.trans, is.tt, isInteractionType, makeGenomicInteractionsFromFile, name, plotAvgViewpoint, plotCisTrans, plotCounts, plotDists, plotInteractionAnnotations, plotSummaryStats, plotViewpoint, removeDups, resetAnnotations, subsetByFeatures, summariseByFeaturePairs, summariseByFeatures, viewPoint ExportMethods: updateObject, summariseByFeatures, summariseByFeaturePairs, sum, subsetByFeatures, resetAnnotations, name, isInteractionType, is.tt, is.trans, is.pt, is.pp, is.pd, is.dt, is.dd, is.cis, interactionCounts, export.igraph, export.chiasig, export.bedpe, export.bed12, description, countsBetweenAnchors, calculateDistances, asBED, annotationFeatures, annotateRegions, annotateInteractions, anchorTwo, anchorOne, name<-, interactionCounts<-, description<- ExportClasses: GenomicInteractions Package: GenomicOZone Exports: GOZDataSet, GenomicOZone, extract_genes, extract_outstanding_zones, extract_zone_expression, extract_zones, plot_chromosomes, plot_genome, plot_zones Package: GenomicRanges Exports: as.data.frame.GPos, duplicated.GenomicRanges, sort.GenomicRanges, sort.GRangesList, summary.GenomicRanges, phicoef, GRanges, .DollarNames.GenomicRanges, .DollarNames.GRanges, GPos, from_GPos_to_GRanges, GRangesFactor, GNCList, GenomicRangesList, GRangesList, makeGRangesFromDataFrame, makeGRangesListFromDataFrame, makeGRangesListFromFeatureFragments, isSmallGenome, absoluteRanges, relativeRanges, tileGenome, bindAsGRanges, mcolAsRleList, binnedAverage, checkConstraint, granges, grglist ExportMethods: checkConstraint, granges, grglist, length, names, names<-, [, [<-, $, $<-, as.character, as.factor, as.data.frame, coerce, show, split, unlist, range, Ops, merge, summary, update, duplicated, match, is.unsorted, order, sort, rank, union, intersect, setdiff, start, start<-, end, end<-, width, width<-, strand, strand<-, invertStrand, score, score<-, updateObject, bindROWS, parallelSlotNames, elementMetadata, elementMetadata<-, mcols, mcols<-, values, values<-, pcompare, selfmatch, FactorToClass, relistToClass, ranges, ranges<-, rglist, pos, findOverlaps, countOverlaps, windows, update_ranges, shift, narrow, resize, flank, promoters, restrict, trim, reduce, gaps, disjoin, isDisjoint, disjointBins, coverage, punion, pintersect, psetdiff, pgap, precede, follow, nearest, distance, distanceToNearest, tile, slidingWindows, seqinfo, seqinfo<-, seqnames, seqnames<- ExportClasses: Constraint, Constraint_OR_NULL, GenomicRanges, GenomicRanges_OR_missing, GenomicPos, IRanges_OR_IPos, GRanges, GPos, UnstitchedGPos, StitchedGPos, GRangesFactor, DelegatingGenomicRanges, GNCList, GenomicRangesList, GenomicRanges_OR_GenomicRangesList, SimpleGenomicRangesList, CompressedGenomicRangesList, GRangesList, SimpleGRangesList, CompressedGRangesList, GenomicRanges_OR_GRangesList Package: GenomicScores Exports: GScores, availableGScores, getGScores, makeGScoresPackage ExportMethods: citation, name, type, organism, provider, providerVersion, referenceGenome, score, scores, gscores, qfun, dqfun, seqinfo, seqlengths, seqlevelsStyle, seqnames, gscoresNonSNRs, populations, defaultPopulation, defaultPopulation<-, gscoresTag, gscoresTag<-, gscoresGroup, gscoresGroup<-, nsites, show ExportClasses: GScores Package: GenomicTuples Exports: tuples<-, GTuples, GTuplesList, IPD, duplicated.GTuples, gtlist, gtuples, size, sort.GTuples, tuples ExportMethods: union, tuples, tile, sort, size, show, shift, setdiff, selfmatch, restrict, resize, relistToClass, reduce, range, punion, psetdiff, promoters, pintersect, pgap, pcompare, order, narrow, match, isDisjoint, is.unsorted, intersect, granges, gaps, flank, findOverlaps, duplicated, disjointBins, disjoin, coverage, countOverlaps, c, as.data.frame, Ops, IPD, tuples<-, [<- ExportClasses: GTuplesList, GTuples Package: genoset Exports: chrNames, chrNames<-, GenoSet, RleDataFrame, baf2mbaf, boundingIndices, boundingIndicesByChr, bounds2Rle, calcGC, calcGC2, chr, chrIndices, chrInfo, chrOrder, chrPartitioning, cn2lr, fixSegNAs, gcCorrect, genoPlot, genoPos, genomeAxis, isGenomeOrder, lengths, lr2cn, modeCenter, nrow, numCallable, pos, rangeColMeans, rangeMaxs, rangeMeans, rangeMins, rangeSampleMeans, rangeSegMeanLength, rangeSums, rangeWhichMaxs, rangeWhichMins, rbindDataframe, readGenoSet, runCBS, segPairTable, segTable, segs2Granges, segs2Rle, segs2RleDataFrame, toGenomeOrder ExportMethods: show, rowSums, rowMeans, colSums, colMeans, as.matrix, [<-, [ ExportClasses: RleDataFrame, GenoSetOrGenomicRanges, GenoSet Package: genotypeeval Exports: GoldDataFromGRanges, GoldDataParam, ReadGoldData, ReadVCFData, ReadVCFDataChunk, VCFEvaluate, VCFQAParam, didSamplePass, didSamplePassOverall, getName, getPlots, getResults, getVR Package: genphen Exports: runGenphen, runDiagnostics, runPhyloBiasCheck Package: GenRank Exports: CombP, ComputeCE, ComputeRP Package: GenVisR Exports: Clinical, GMS, Lolliplot, MutSpectra, MutationAnnotationFormat, Rainfall, TvTi, VEP, Waterfall, cnFreq, cnSpec, cnView, compIdent, covBars, genCov, geneViz, ideoView, lohSpec, lohView, lolliplot, waterfall ExportMethods: writeData, getVersion, getSample, getPosition, getPath, getMutation, getMeta, getHeader, getGrob, getDescription, getData, drawPlot ExportClasses: Waterfall, VEP, Rainfall, MutationAnnotationFormat, MutSpectra, Lolliplot, GMS, Clinical Package: GEOquery Exports: GDS2MA, GDS2eSet, getGEO, getGEOSuppFiles, getGEOfile, getGSEDataTables, gunzip, parseGEO ExportMethods: show, dataTable, Table, Meta, GSMList, GPLList, GPL, Columns, Accession Package: GEOsubmission Exports: microarray2soft Package: gep2pep Exports: CategorizedCollection, CondSEA, PathSEA, addSingleGeneSets, as.CategorizedCollection, buildPEPs, checkRepository, clearCache, createMergedRepository, createRepository, exportSEA, gene2pathways, getCollections, getDetails, getResults, importFromRawMode, importMSigDB.xml, loadCollection, loadESmatrix, loadPVmatrix, loadSampleGEP, loadSamplePWS, makeCollectionIDs, openRepository, setId2setName ExportClasses: CategorizedCollection Package: gespeR Exports: path<-, Phenotypes, TargetRelations, annotate.gsp, concordance, gsp, join, lasso.rand, loadValues, na.rem, rbo, ssp, stability, stability.selection, target.relations, unloadValues, values, writeValues ExportMethods: scores, gespeR, c, as.data.frame ExportClasses: gespeR, TargetRelations, Phenotypes Package: GEWIST Exports: effectPDF, gewistLevene Package: GGBase Exports: getSS, make_smlSet, combine, dropMonomorphies, nsFilter, MAFfilter, GTFfilter, clipPCs, regressOut, combine, smList, exprs, externalize, plot_EvG, genesym, rsid, probeId, permEx, allsnps, featureNames, featureData ExportMethods: genesym, rsid, probeId, plot_EvG, permEx, clipPCs ExportClasses: smlSet, probeId, rsid Package: ggbio Exports: arrangeGrobByParsingLegend, ggbio, GGbio, scale_x_sequnit, scale_fill_giemsa, scale_fill_fold_change, circle, tracks, align.plots, alignPlots, plotFragLength, plotSpliceSum, plotStackedOverview, plotKaryogram, plotIdeogram, Ideogram, plotGrandLinear, plotRangesLinkedToData, theme_null, theme_alignment, theme_clear, theme_tracks_sunset, theme_pack_panels, theme_noexpand, theme_genome, ggsave, zoom, zoom_in, zoom_out, nextView, prevView ExportMethods: cbind, rbind, layout_karyogram, layout_circle, stat_aggregate, stat_coverage, stat_identity, stat_mismatch, stat_stepping, stat_gene, stat_table, stat_slice, stat_bin, stat_reduce, geom_chevron, geom_arch, geom_alignment, geom_arrow, geom_arrowrect, geom_rect, geom_bar, geom_segment, autoplot, rescale, fixed, fixed<-, xlim, xlim<-, reset, backup, bgColor, bgColor<-, labeled, labeled<-, mutable, mutable<-, height, height<-, hasAxis, hasAxis<- ExportClasses: GGbio, Ideogram, Plot, Tracked, Tracks, Grob Package: ggcyto Exports: %+%, .fr2dt, .fs2dt, as.ggplot, autoplot, axis_x_inverse_trans, axis_y_inverse_trans, compute_stats, flowCore_asinht_trans, fortify_fs, geom_gate, geom_hvline, geom_overlay, geom_stats, getFlowFrame, ggcyto, ggcyto_arrange, ggcyto_par_default, ggcyto_par_set, is.ggcyto, is.ggcyto_flowSet, is.ggcyto_par, labs_cyto, marginalFilter, rescale_gate, scale_x_flowCore_fasinh, scale_x_flowJo_biexp, scale_x_flowJo_fasinh, scale_x_flowjo_biexp, scale_x_flowjo_fasinh, scale_x_logicle, scale_y_flowCore_fasinh, scale_y_flowJo_biexp, scale_y_flowJo_fasinh, scale_y_flowjo_biexp, scale_y_flowjo_fasinh, scale_y_logicle, stat_position ExportMethods: transform, show, print, +, %+% ExportClasses: ggcyto_flowSet, ggcyto_GatingSet, ggcyto_GatingLayout, ggcyto Package: GGtools Exports: TabixFile, gwSnpTests, topSnps, eqtlTests, topFeats, getCisMap, pData, plot, best.cis.eQTLs, chromsUsed, fullreport, eqtlEstimates, probesManaged, snpsManaged, topScores, topGenes, locusNames, geneNames, geneIndcol, nthScores, vcf2sm, fdr, transScores, getBest, getAll, getCall, transTab, meqtlTests, meta.best.cis.eQTLs, meta.All.cis.eQTLs, meta.transScores, annotation, sensanal, snplocsDefault, richNull, meta.bindmaf, meta.richNull, pifdr, All.cis, collectBest, collectFiltered, cis.FDR.filter.SNPcentric, cis.FDR.filter.best, eqBox, eqDesc, best.trans.eQTLs, chrFilter, All.cis, chrnames, chrnames<-, estimates, estimates<-, excludeRadius, excludeRadius<-, exFilter, exFilter<-, folderStem, folderStem<-, gchrpref, gchrpref<-, geneannopk, geneannopk<-, geneApply, geneApply<-, keepMapCache, keepMapCache<-, nperm, nperm<-, radius, radius<-, rhs, rhs<-, schrpref, schrpref<-, shortfac, shortfac<-, smchrpref, smchrpref<-, smFilter, smFilter<-, smpack, smpack<-, snpannopk, snpannopk<-, SSgen, SSgen<-, cis.FDR.filter.SNPcentric.complete, binqq, qqhex, gffprocess, simpleTiling, cgff2dt, ciseqByCluster, scoresCis, binnedQQ, transeqByCluster, transeqByChrom, cisScores, concatCis, eqtlTests.me, plotsens, inflammFilter, update_fdr_filt, filtgen.maf.dist, eqsens_dt, genome<-, buildConfList, add878, addgwhit, cisAssoc, sampsInVCF, appraise ExportMethods: calfig, snpchr, snpchr<-, gbufsize, gbufsize<-, batchsize, batchsize<-, extraProps, extraProps<-, chrnames, chrnames<-, estimates, estimates<-, excludeRadius, excludeRadius<-, exFilter, exFilter<-, folderStem, folderStem<-, gchrpref, gchrpref<-, geneannopk, geneannopk<-, geneApply, geneApply<-, keepMapCache, keepMapCache<-, nperm, nperm<-, radius, radius<-, rhs, rhs<-, schrpref, schrpref<-, shortfac, shortfac<-, smchrpref, smchrpref<-, smFilter, smFilter<-, smpack, smpack<-, snpannopk, snpannopk<-, SSgen, SSgen<-, gwSnpTests, show, topFeats, plot, transTab ExportClasses: EqAppr, eqtlTestsManager, eqtlEstimatesManager, mcwBestCis, gwSnpScreenResult, transManager, allSigCis, sensiCisInput, sensiCisOutput, mcwAllCis, cisRun, CisConfig, TransConfig Package: ggtree Exports: %+>%, %<%, %<+%, %>%, ., Date2decimal, GeomHilight, MRCA, StatBalance, StatHilight, add_colorbar, aes, annotation_image, arrow, as.polytomy, collapse, decimal2Date, expand, facet_data, facet_labeller, facet_plot, facet_widths, flip, fortify, geom_aline, geom_balance, geom_cladelabel, geom_cladelabel2, geom_facet, geom_hilight, geom_hilight_encircle, geom_inset, geom_label, geom_label2, geom_motif, geom_nodelab, geom_nodelab2, geom_nodepoint, geom_point, geom_point2, geom_range, geom_rootedge, geom_rootpoint, geom_segment2, geom_strip, geom_taxalink, geom_text, geom_text2, geom_tiplab, geom_tiplab2, geom_tippoint, geom_tree, geom_tree2, geom_treescale, get.path, get_clade_position, get_heatmap_column_position, get_taxa_name, ggdensitree, ggplot, ggsave, ggtree, gheatmap, groupClade, groupOTU, gzoom, inset, layout_circular, layout_dendrogram, layout_fan, layout_rectangular, msaplot, multiplot, nodebar, nodeid, nodelab, nodepie, open_tree, phylopic, range_format, read.tree, revts, rotate, rotate_tree, rtree, scaleClade, scale_color, scale_x_ggtree, scale_x_range, set_hilight_legend, stat_hilight, subview, theme, theme_dendrogram, theme_inset, theme_tree, theme_tree2, unit, viewClade, xlim, xlim_expand, xlim_tree ExportMethods: scale_color, gzoom Package: GIGSEA Exports: dataframe2geneSet, geneSet2Net, geneSet2sparseMatrix, gmt2geneSet, matrixPval, orderedIntersect, permutationMultipleLm, permutationMultipleLmMatrix, permutationSimpleLm, permutationSimpleLmMatrix, runGIGSEA, weightedGSEA, weightedMultipleLm, weightedPearsonCorr Package: girafe Exports: AlignedGenomeIntervals, plotAligned, trimAdapter, perWindow, fracOverlap, intPhred, coverageOneStrand, addNBSignificance, plotNegBinomFit, medianByPosition, agiFromBam, getFeatureCounts, countReadsAnnotated, chrlengths, clusters, coerce, plot, sample, subset, summary ExportMethods: plot, [, interval_overlap, interval_included, chrlengths, chrlengths<-, chromosome, coerce, coverage, clusters, detail, export, extend, hist, nchar, matches, matches<-, id, id<-, organism, organism<-, reads, reads<-, reduce, sample, score, score<-, seqnames, show, sort, strand, strand<-, subset, summary, width, which_nearest ExportClasses: AlignedGenomeIntervals Package: GISPA Exports: GISPA, computePS, cptModel, cptPlot, cptSlopeplot, propBarplot, stackedBarplot Package: GladiaTOX Exports: assignDefaultMthds, buildAssayTab, deleteStudy, exportResultForToxpiGUI, exportResultTable, glComputeToxInd, glPlotPie, glPlotPieLogo, glPlotPosCtrl, glPlotStat, glPlotToxInd, gtoxAICProb, gtoxAddModel, gtoxCalcVmad, gtoxCode2CASN, gtoxConf, gtoxConfDefault, gtoxConfList, gtoxConfLoad, gtoxConfReset, gtoxConfSave, gtoxFit, gtoxHillACXX, gtoxHillConc, gtoxHillVal, gtoxImportThermoDB, gtoxListFlds, gtoxLoadAcid, gtoxLoadAeid, gtoxLoadAid, gtoxLoadApid, gtoxLoadAsid, gtoxLoadChem, gtoxLoadClib, gtoxLoadData, gtoxLoadVehicle, gtoxLoadVmad, gtoxLoadWaid, gtoxMakeAeidPlts, gtoxMthdAssign, gtoxMthdClear, gtoxMthdList, gtoxMthdLoad, gtoxObjCnst, gtoxObjGnls, gtoxObjHill, gtoxPlotErrBar, gtoxPlotFitc, gtoxPlotFits, gtoxPlotM4ID, gtoxPlotPie, gtoxPlotPieLgnd, gtoxPlotPlate, gtoxPlotWin, gtoxPrepOtpt, gtoxQuery, gtoxRegister, gtoxReport, gtoxRun, gtoxSendQuery, gtoxSetWllq, gtoxSubsetChid, gtoxUpdate, gtoxWriteData, loadAnnot, lu, lw, prepareDatForDB Package: Glimma Exports: as.hexcol, glMDPlot, glMDRmd, glMDSPlot, glXYPlot Package: glmSparseNet Exports: buildLambda, buildStringNetwork, cv.glmDegree, cv.glmHub, cv.glmOrphan, cv.glmSparseNet, degreeCor, degreeCov, degreeSparsebn, ensemblGeneNames, geneNames, glmDegree, glmHub, glmOrphan, glmSparseNet, hallmarks, heuristicScale, hubHeuristic, networkCorParallel, networkCovParallel, networkOptions, orphanHeuristic, protein2EnsemblGeneNames, separate2GroupsCox, stringDBhomoSapiens Package: GlobalAncova Exports: gGlobalAncova, GAGO, GAKEGG, GABroad, GlobalAncova.decomp, gGlobalAncova.hierarchical, pair.compare, Plot.features, Plot.sequential, Plot.all ExportMethods: sigEndnodes, results, Plot.hierarchy, GlobalAncova, GlobalAncova.closed, Plot.genes, Plot.subjects ExportClasses: GAhier Package: globalSeq Exports: cursus, intern.chromo, intern.conva, intern.cov, intern.crude, intern.estim, intern.focus, intern.matrix, intern.permu, intern.plot, intern.sam, intern.score, intern.select, omnibus, proprius Package: globaltest Exports: gt, mlogit, gtGO, combine, leafNodes, draw, gtKEGG, gtBroad, gtConcept, comparative, focusLevel, inheritance, covariates, features, subjects, gt.options, findFocus, gtPS, gtKS, gtLI, bbase, btensor, reparamZ, reweighZ ExportMethods: [, [[, show, result, p.value, length, names, names<-, sort, size, hist, z.score, summary, residuals, fitted.values, coefficients, alias, alias<-, model.matrix, weights, p.adjust, subsets, extract, sterms ExportClasses: mlogit, gt.object Package: gmapR Exports: bam_tally, GmapGenome, GmapGenomeDirectory, GsnapParam, directory, BamTallyParam, makeGmapGenomePackage, GsnapOutput, GmapSnps, GmapSnpDirectory, TP53Genome, TP53Which, variantSummary, GmapParam, cmetindex ExportMethods: bamPaths, path, genome, seqinfo, gsnap, snps<-, spliceSites<-, getSeq, gmap ExportClasses: GmapGenome, GmapGenomeDirectory, GmapSnpDirectory, GsnapOutput, GmapSnps, BamTallyParam, GsnapParam, GmapParam, GmapAlignerParam Package: GmicR Exports: Auto_WGCNA, Batch_Net, Data_Prep, GO_Module_NameR, GSEAGO_Builder, Gmic_viz, InverseARCs, Query_Prep, bn_tabu_gen, xCell_loader Package: GMRP Exports: fmerge, chrp, mktable, path, pathdiagram, pathdiagram2, snpPositAnnot, ucscannot Package: GNET2 Exports: build_module, build_moduleR, build_split_table, build_moduleR_heuristic, calc_likelihood_score, get_correlation_list, gnet, kneepointDetection, plot_gene_group, plot_group_correlation, plot_tree, extract_edges Package: GOexpress Exports: cluster_GO, expression_plot, expression_plot_symbol, expression_profiles, expression_profiles_symbol, GO_analyse, heatmap_GO, hist_scores, list_genes, plot_design, pValue_GO, quantiles_scores, rerank, subEset, subset_scores, table_genes Package: GOfuncR Exports: go_enrich, get_names, get_anno_genes, get_child_nodes, get_parent_nodes, get_anno_categories, get_ids, plot_anno_scores, refine Package: GOFunction Exports: GOFunction Package: GOpro Exports: findGO 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, equivClust, iterEquivClust, equivClust2pdf Package: GOSemSim Exports: clusterSim, combineScores, geneSim, goSim, godata, load_OrgDb, mclusterSim, mgeneSim, mgoSim, termSim ExportClasses: GOSemSimDATA Package: goseq Exports: getgo, getlength, goseq, makespline, nullp, plotPWF, supportedOrganisms Package: GOSim Exports: getOffsprings, getAncestors, getParents, getChildren, setEvidenceLevel, setOntology, getGOInfo, filterGO, getGeneSim, getGeneFeaturesPrototypes, getGeneSimPrototypes, selectPrototypes, setEnrichmentFactors, getGOGraph, getGOGraphsGenes, calcICs, getMinimumSubsumer, getDisjCommAnc, getTermSim, evaluateClustering, GOenrichment, getGeneFeatures, calc.diffusion.kernel, load.diffusion.kernel Package: goSTAG Exports: annotateClusters, groupClusters, loadGeneLists, loadGOTerms, performGOEnrichment, performHierarchicalClustering, plotHeatmap Package: GOstats Exports: compCorrGraph, compGdist, enumPairs, GOGraph, idx2dimnames, isTriad, makeGOGraph, notConn, oneGOGraph, reduce2Degreek, shortestPath, simLL, simLP, simUI, triadCensus, probeSetSummary, termGraphs, inducedTermGraph, plotGOTermGraph ExportMethods: hyperGTest, pvalues, description, oddsRatios, expectedCounts, htmlReport, goDag, geneCounts, universeCounts, geneIds, geneIdUniverse, universeMappedCount, geneMappedCount, annotation, testName, summary ExportClasses: GOHyperGResult Package: GOsummaries Exports: add_expression.gosummaries, add_to_slot.gosummaries, customize, gosummaries, is.gosummaries, panel_boxplot, panel_boxplot_classes, panel_violin, panel_violin_box, panel_violin_box_classes, panel_violin_classes, plotWordcloud Package: GOTHiC Exports: pairReads, mapReadsToRestrictionSites, GOTHiC, GOTHiChicup Package: gpart Exports: BigLD, CLQD, GPART, LDblockHeatmap, convert2GRange Package: gpls Exports: gpls, glpls1a, glpls1a.cv.error, glpls1a.train.test.error, glpls1a.mlogit, glpls1a.logit.all, glpls1a.mlogit.cv.error Package: gQTLBase Exports: ciseStore, storeToFf, extractByProbes, extractByRanges, storeMapResults, extractBySymbols, storeApply, loadAndFilterResult, mergeCIstates, mergeGWhits, ufeatByTiling, balancedFeatList, describeStore, describeByFilts, matprint ExportMethods: extractByProbes, extractByRanges, extractBySymbols, show ExportClasses: storeDescription, ciseStore Package: gQTLstats Exports: cisAssoc, clipPCs, regressOut, AllAssoc, pifdr, storeToQuantiles, storeToHist, storeToFDR, storeToFDRByProbe, storeToMaxAssocBySNP, getFDRfunc, getTab, setFDRfunc, directPlot, txsPlot, eqBox2, eqDesc2, enumerateByFDR, manhWngr, eqBox3, table_sensobj_thresh, queryVCF, senstab, prep.cisAssocNB, cisCount, qqStore, transAssoc, TransChunk, filteredDFwPerm, transTable, mixedVCFtoSnpMatrix, cisEsts, gQTLs, gQTLswarm, describe, TransStore, tsByRank_sing, transBrowse, tsByRankAccum_sing, transBrowse2, eqBox3, pifdr2, tsIndex.reg, tqbrowser, pifdr3, collapse_multiPerm, distToGene, getTransRegistries, tsByRankAccum ExportClasses: TransStore, TransChunk, FDRsupp Package: gramm4R Exports: preGramm, naiveGramm, nlfitGramm, Gramm Package: graper Exports: getPIPs, graper, makeExampleData, makeExampleDataWithUnequalGroups, plotELBO, plotGroupPenalties, plotPosterior Package: graph Exports: graphNEL, graphAM, boundary, buildRepDepGraph, calcProb, calcSumProb, duplicatedEdges, graph2SparseM, listEdges, randomEGraph, randomGraph, randomNodeGraph, validGraph, eWV, pathWeights, .dropEdges, aveNumEdges, sparseM2Graph, gxlTreeNEL, ftM2adjM, ftM2graphNEL, .ftM2other, int2ftM, ftM2int, aM2bpG, mostEdges, numNoEdges, reverseEdgeDirections, ugraphOld, graph.par, graph.par.get, graphRenderInfo, nodeRenderInfo, edgeRenderInfo, parRenderInfo, nodeRenderInfo<-, edgeRenderInfo<-, parRenderInfo<-, graphRenderInfo<-, toDotWithRI, graphBAM, MultiGraph, eweights, edgeSetIntersect0, edgeSetUnion0, extractFromTo, subsetEdgeSets, extractGraphAM, extractGraphBAM, mgEdgeData, mgEdgeData<- ExportMethods: DFS, Dist, acc, addEdge, addNode, adj, adjacencyMatrix, clearNode, clusteringCoefficient, combineNodes, complement, connComp, degree, dumpGXL, edgeL, edgeMatrix, edgeNames, edgeWeights, edgemode, edgemode<-, edges, nodes<-, fromGXL, inEdges, initialize, intersection, intersection2, isAdjacent, isConnected, isDirected, join, nodes, numNodes, numEdges, plot, removeEdge, removeNode, show, subGraph, threshold, toGXL, union, validateGXL, coerce, toDotR, attrDefaults, attrDefaults<-, edgeDataDefaults, edgeDataDefaults<-, mgEdgeDataDefaults, mgEdgeDataDefaults<-, nodeDataDefaults, nodeDataDefaults<-, edgeData, edgeData<-, nodeData, nodeData<-, attrDataItem, attrDataItem<-, removeAttrDataItem<-, ugraph, leaves, updateGraph, extractFromTo, graphIntersect, graphUnion, removeEdgesByWeight, edgeSets ExportClasses: distGraph, clusterGraph, graph, graphNEL, graphAM, attrData, simpleEdge, edgeSet, edgeSetNEL, edgeSetAM, multiGraph, renderInfo, MultiGraph, graphBAM, graphBase Package: GraphAlignment Exports: LinearAssignment, ComputeM, AlignNetworks, CreateScoreMatrix, InvertPermutation, Permute, Trace, InitialAlignment, GetBinNumber, VectorToBin, MatrixToBin, ComputeScores, GenerateExample, ComputeLinkParameters, ComputeNodeParameters, EncodeDirectedGraph, AnalyzeAlignment, AlignedPairs, .Last.lib Package: GraphAT Exports: clust2Mat, getpvalue, makeClustM, mat2UndirG, permEdgesM2M, permNodesM2M, permPower Package: graphite Exports: pathways, pathwayDatabases, pathwayId, pathwayTitle, pathwayDatabase, pathwaySpecies, pathwayTimestamp, pathwayURL, buildPathway, cytoscapePlot, pathwayGraph, runSPIA ExportMethods: convertIdentifiers, plot, runClipper, prepareSPIA, runTopologyGSA, edgeData, edgeData<-, edgeDataDefaults<-, edges, nodes ExportClasses: Pathways, PathwayList, Pathway Package: GraphPAC Exports: Find.TSP.Path, GraphClust, Plot.Protein Package: GreyListChIP Exports: greyListBS ExportMethods: getKaryotype, loadKaryotype, setRegions, countReads, calcThreshold, makeGreyList, export, show ExportClasses: GreyList Package: GRmetrics Exports: GRbox, GRdrawDRC, GRfit, GRgetDefs, GRgetGroupVars, GRgetMetrics, GRgetValues, GRscatter Package: groHMM Exports: writeWiggle, detectTranscripts, makeConsensusAnnotations, evaluateHMMInAnnotations, windowAnalysis, breakTranscriptsOnGenes, combineTranscripts, getTxDensity, limitToXkb, runMetaGene, metaGene, pausingIndex, polymeraseWave, getCores, averagePlot, countMappableReadsInInterval, expressedGenes, metaGeneMatrix, metaGene_nL, readBed, RgammaMLE, Rnorm, Rnorm.exp, tlsDeming, tlsLoess, tlsSvd Package: GSALightning Exports: GSALight, permTestLight, wilcoxTest Package: GSAR Exports: AggrFtest, HDP.ranking, radial.ranking, WWtest, KStest, MDtest, RKStest, RMDtest, GSNCAtest, findMST2, findMST2.PPI, plotMST2.pathway, TestGeneSets Package: GSCA Exports: GSCAplot, GSCA, GSCAeda, annotatePeaks, tabSearch, ConstructTG, GSCAui Package: gscreend Exports: GeneData, ResultsTable, RunGscreend, createPoolScreenExp, plotModelParameters, plotReplicateCorrelation, sgRNAData ExportMethods: sgRNAData, GeneData ExportClasses: PoolScreenExp Package: GSEABase Exports: NullIdentifier, ENSEMBLIdentifier, EnzymeIdentifier, GenenameIdentifier, RefseqIdentifier, SymbolIdentifier, UnigeneIdentifier, UniprotIdentifier, EntrezIdentifier, AnnotationIdentifier, AnnoOrEntrezIdentifier, GOAllFrameIdentifier, NullCollection, ExpressionSetCollection, ComputedCollection, KEGGCollection, OMIMCollection, PMIDCollection, ChrCollection, ChrlocCollection, MapCollection, PfamCollection, PrositeCollection, GOCollection, OBOCollection, BroadCollection, asBroadUri, getBroadSets, toBroadXML, getGmt, toGmt, getOBOCollection, geneIds, geneIds<-, ontology ExportMethods: show, coerce, details, initialize, intersect, union, setdiff, &, |, Logic, incidence, mapIdentifiers, annotation, annotation<-, ids, bcCategory, bcSubCategory, evidenceCode, ontology, subsets, goSlim, GeneSet, geneIdType, geneIds, setIdentifier, setName, description, longDescription, organism, pubMedIds, urls, contributor, setVersion, creationDate, collectionType, geneIdType<-, geneIds<-, setIdentifier<-, setName<-, description<-, longDescription<-, organism<-, pubMedIds<-, urls<-, contributor<-, setVersion<-, creationDate<-, collectionType<-, GeneColorSet, phenotype, geneColor, phenotypeColor, coloring, phenotype<-, geneColor<-, phenotypeColor<-, coloring<-, GeneSetCollection, updateObject, names, [, [[ ExportClasses: GeneIdentifierType, NullIdentifier, AnnotationIdentifier, ENSEMBLIdentifier, EntrezIdentifier, EnzymeIdentifier, GenenameIdentifier, RefseqIdentifier, SymbolIdentifier, UnigeneIdentifier, UniprotIdentifier, GOAllFrameIdentifier, CollectionType, NullCollection, ExpressionSetCollection, ComputedCollection, CollectionIdType, KEGGCollection, OMIMCollection, PMIDCollection, ChrCollection, ChrlocCollection, MapCollection, PfamCollection, PrositeCollection, GOCollection, OBOCollection, BroadCollection, GeneSet, GeneColorSet, GeneSetCollection Package: GSEABenchmarkeR Exports: bpPlot, cacheResource, compOpt, compRand, evalNrSets, evalNrSigSets, evalRandomGS, evalRelevance, evalTypeIError, loadEData, maPreproc, metaFC, plotDEDistribution, plotNrSamples, readDataId2diseaseCodeMap, readResults, runDE, runEA, writeDE Package: GSEAlm Exports: lmPerGene, gsealmPerm, resplot, restrip, CooksDPerGene, dfbetasPerGene, dffitsPerGene, Leverage, getResidPerGene, mnDiffPlot, GSNormalize, identity, one Package: GSReg Exports: GSReg.GeneSets.EVA, GSReg.GeneSets.DIRAC, GSReg.kendall.tau.distance.restricted, GSReg.kendall.tau.distance.template, GSReg.kendall.tau.distance, GSReg.overlapJunction, GSReg.SEVA Package: GSRI Exports: rowt, rowF ExportMethods: gsri, getGsri, getCdf, getParms, export, show, summary, plot, readCls, readGct, sortGsri ExportClasses: Gsri Package: GSVA Exports: igsva ExportMethods: gsva, filterGeneSets, computeGeneSetsOverlap Package: gtrellis Exports: add_heatmap_track, add_ideogram_track, add_lines_track, add_points_track, add_rect_track, add_segments_track, add_track, current_track, get_cell_meta_data, gtrellis_layout, gtrellis_show_index Package: GUIDEseq Exports: GUIDEseqAnalysis, getUniqueCleavageEvents, getPeaks, combineOfftargets, mergePlusMinusPeaks, offTargetAnalysisOfPeakRegions, annotateOffTargets, createBarcodeFasta, getUsedBarcodes Package: Guitar Exports: GuitarPlot, makeGuitarTxdb, samplePoints Package: Gviz Exports: .chrName, .doCache, AlignedReadTrack, AlignmentsTrack, AnnotationTrack, DetailsAnnotationTrack, BiomartGeneRegionTrack, CustomTrack, DataTrack, DisplayPars, SequenceTrack, OverlayTrack, drawAxis, drawGD, GeneRegionTrack, GenomeAxisTrack, HighlightTrack, IdeogramTrack, UcscTrack, addScheme, as.list, availableDefaultMapping, availableDisplayPars, clearSessionCache, exportTracks, getScheme, plotTracks ExportMethods: [, as.list, chromosome, chromosome<-, coerce, consolidateTrack, coords, coverage, displayPars, displayPars<-, end, end<-, exon, exon<-, feature, feature<-, gene, gene<-, genome, genome<-, getPar, group, group<-, head, identifier, identifier<-, imageMap, initialize, length, max, min, names, names<-, position, range, ranges, score, seqnames, seqlevels, seqinfo, setPar, split, stacking, stacking<-, stacks, start, start<-, strand, strand<-, subseq, subset, symbol, symbol<-, tags, tail, transcript, transcript<-, values, values<-, width, width<- ExportClasses: AlignedReadTrack, AlignmentsTrack, AnnotationTrack, DetailsAnnotationTrack, BiomartGeneRegionTrack, DataTrack, DisplayPars, GdObject, GeneRegionTrack, GenomeAxisTrack, IdeogramTrack, ImageMap, NumericTrack, RangeTrack, SequenceTrack, StackedTrack, HighlightTrack, OverlayTrack, CustomTrack Package: gwascat Exports: locs4trait, topTraits, chklocs, riskyAlleleCount, getRsids, getTraits, subsetByChromosome, subsetByTraits, obo2graphNEL, makeCurrentGwascat, traitsManh, gwcex2gviz, bindcadd_snv, show, ldtagr, uri2node, node2uri, metadata ExportMethods: getRsids, [, getTraits, subsetByChromosome, subsetByTraits, show ExportClasses: gwaswloc Package: GWASTools Exports: SnpAnnotationDataFrame, SnpAnnotationSQLite, ScanAnnotationDataFrame, ScanAnnotationSQLite, NcdfReader, NcdfGenotypeReader, NcdfIntensityReader, GdsReader, GdsGenotypeReader, GdsIntensityReader, MatrixGenotypeReader, GenotypeData, IntensityData, GenotypeIterator, GenotypeBlockIterator, alleleFrequency, anomSegmentBAF, anomFilterBAF, anomDetectBAF, anomDetectLOH, anomIdentifyLowQuality, anomSegStats, anomStatsPlot, apartSnpSelection, asSnpMatrix, assocCoxPH, assocRegression, BAFfromClusterMeans, BAFfromGenotypes, batchChisqTest, batchFisherTest, checkGenotypeFile, checkImputedDosageFile, checkIntensityFile, checkNcdfGds, chromIntensityPlot, convertGdsNcdf, convertNcdfGds, createDataFile, createAffyIntensityFile, dupDosageCorAcrossDatasets, duplicateDiscordance, duplicateDiscordanceAcrossDatasets, duplicateDiscordanceProbability, exactHWE, findBAFvariance, gdsSubset, gdsSubsetCheck, genoClusterPlot, genoClusterPlotByBatch, genotypeToCharacter, hetByScanChrom, hetBySnpSex, ibdAreasDraw, ibdAssignRelatedness, ibdAssignRelatednessKing, ibdPlot, imputedDosageFile, intensityOutliersPlot, kingIBS0FSCI, manhattanPlot, meanIntensityByScanChrom, meanSdByChromWindow, medianSdOverAutosomes, mendelErr, mendelList, mendelListAsDataFrame, minorAlleleDetectionAccuracy, missingGenotypeByScanChrom, missingGenotypeBySnpSex, pedigreeCheck, pedigreeDeleteDuplicates, pedigreeMaxUnrelated, pedigreePairwiseRelatedness, pasteSorted, plinkCheck, plinkWrite, pseudoautoIntensityPlot, qqPlot, qualityScoreByScan, qualityScoreBySnp, sdByScanChromWindow, setMissingGenotypes, simulateGenotypeMatrix, simulateIntensityMatrix, snpCorrelationPlot, vcfCheck, vcfWrite, genoDataAsVCF, allequal, getobj, saveas, readWriteFirst ExportMethods: getAlleleA, getAlleleB, getAnnotation, getAttribute, getBAlleleFreq, getChromosome, getDimension, getDimensionNames, getGenotype, getGenotypeSelection, getLogRRatio, getMetadata, getNodeDescription, getPosition, getQuality, getQuery, getScanAnnotation, getScanID, getScanVariable, getScanVariableNames, getSex, getSnpAnnotation, getSnpID, getSnpVariable, getSnpVariableNames, getVariable, getVariableNames, getX, getY, hasBAlleleFreq, hasCoordVariable, hasLogRRatio, hasQuality, hasScanAnnotation, hasScanVariable, hasSex, hasSnpAnnotation, hasSnpVariable, hasVariable, hasX, hasY, nsnp, nscan, writeAnnotation, writeMetadata, autosomeCode, XchromCode, YchromCode, XYchromCode, MchromCode, snpFilter, lastFilter, lastFilter<-, iterateFilter, currentFilter, resetIterator, open, close, show ExportClasses: SnpAnnotationDataFrame, SnpAnnotationSQLite, ScanAnnotationDataFrame, ScanAnnotationSQLite, NcdfReader, NcdfGenotypeReader, NcdfIntensityReader, GdsReader, GdsGenotypeReader, GdsIntensityReader, MatrixGenotypeReader, GenotypeData, IntensityData, GenotypeIterator, GenotypeBlockIterator Package: gwasurvivr Exports: gdsCoxSurv, impute2CoxSurv, michiganCoxSurv, plinkCoxSurv, sangerCoxSurv Package: hapFabia Exports: makePipelineFile, hapFabiaVersion, findDenseRegions, matrixPlot, plotIBDsegment, sim, iterateIntervals, identifyDuplicates, analyzeIBDsegments, hapFabia, simulateIBDsegments, split_sparse_matrix, vcftoFABIA, simulateIBDsegmentsFabia, IBDsegmentList, IBDsegment ExportMethods: plot, summary, [[, [[<-, [, [<-, topLZ, plotL, histL, extractIBDsegments, ID, ID<-, bicluster_id, bicluster_id<-, chromosome, chromosome<-, IBDsegmentPos, IBDsegmentPos<-, IBDsegmentLength, IBDsegmentLength<-, numberIndividuals, numberIndividuals<-, numbertagSNVs, numbertagSNVs<-, individuals, individuals<-, tagSNVs, tagSNVs<-, populationIndividuals, populationIndividuals<-, idIndividuals, idIndividuals<-, labelIndividuals, labelIndividuals<-, platformIndividuals, platformIndividuals<-, coreClusterIndividuals, coreClusterIndividuals<-, tagSNVPositions, tagSNVPositions<-, tagSNVAlleles, tagSNVAlleles<-, tagSNVNames, tagSNVNames<-, tagSNVFreq, tagSNVFreq<-, tagSNVGroupFreq, tagSNVGroupFreq<-, tagSNVChange, tagSNVChange<-, tagSNVsPerIndividual, tagSNVsPerIndividual<-, individualPerTagSNV, individualPerTagSNV<-, tagSNVAnno, tagSNVAnno<-, IBDsegments, IBDsegments<-, lengthList, lengthList<-, statistics, statistics<-, setAnnotation, setStatistics, compareIBDsegmentLists, mergeIBDsegmentLists, IBDsegmentList2excel, plotLarger ExportClasses: IBDsegment, IBDsegmentList Package: Harman Exports: arrowPlot, harman, pcaPlot, prcompPlot, reconstructData, shiftBetas ExportClasses: harmanresults Package: Harshlight Exports: HarshComp, HarshExt, Harshlight Package: HCABrowser Exports: HCABrowser ExportMethods: values, undoEsQuery, showBundles, show, results, resetEsQuery, putSubscription, putFile, putCollection, putBundle, pullFiles, pullBundles, postSearch, postBundlesCheckout, per_page, patchCollection, nextResults, headFile, getSubscriptions, getSubscription, getFile, getCollection, getBundlesCheckout, getBundle, fields, deleteSubscription, deleteCollection, deleteBundle, activate ExportClasses: HCABrowser Package: HCAExplorer Exports: HCAExplorer, activate, fields ExportMethods: viewProjects, values, undoQuery, show, results, resetSelect, resetQuery, nextResults, getManifestFileFormats, getManifest, fields, [ ExportClasses: ProjectView, HCAExplorer Package: HDF5Array Exports: DSetHandle, destroy_DSetHandle, get_h5mread_returned_type, h5mread, h5mread_from_reshaped, HDF5ArraySeed, HDF5Array, ReshapedHDF5ArraySeed, ReshapedHDF5Array, setHDF5DumpDir, getHDF5DumpDir, setHDF5DumpFile, getHDF5DumpFile, lsHDF5DumpFile, setHDF5DumpName, getHDF5DumpName, setHDF5DumpChunkLength, getHDF5DumpChunkLength, setHDF5DumpChunkShape, getHDF5DumpChunkShape, getHDF5DumpChunkDim, setHDF5DumpCompressionLevel, getHDF5DumpCompressionLevel, appendDatasetCreationToHDF5DumpLog, showHDF5DumpLog, HDF5RealizationSink, writeHDF5Array, saveHDF5SummarizedExperiment, loadHDF5SummarizedExperiment, quickResaveHDF5SummarizedExperiment, TENxMatrixSeed, TENxMatrix, TENxRealizationSink, writeTENxMatrix, extractNonzeroDataByCol ExportMethods: extractNonzeroDataByCol, dim, dimnames, coerce, show, path, path<-, type, extract_array, sparsity, is_sparse, extract_sparse_array, read_sparse_block, write_sparse_block, write_block, matrixClass, DelayedArray, chunkdim, close ExportClasses: DSetHandle, HDF5ArraySeed, HDF5Array, HDF5Matrix, ReshapedHDF5ArraySeed, ReshapedHDF5Array, ReshapedHDF5Matrix, HDF5RealizationSink, TENxMatrixSeed, TENxMatrix, TENxRealizationSink Package: HDTD Exports: centerdata, covmat.hat, covmat.ts, meanmat.hat, meanmat.ts, orderdata, transposedata Package: heatmaps Exports: coords<-, image<-, label<-, metadata<-, nseq<-, scale<-, CoverageHeatmap, Heatmap, PWMScanHeatmap, PatternHeatmap, coords, default_color, getScale, heatmapOptions, label, metadata, nseq, plotHeatmap, plotHeatmapList, plotHeatmapMeta, plotPatternDensityMap, plot_clusters, plot_legend, scale, smoothHeatmap, xm, ym ExportMethods: ym, xm, width, smoothHeatmap, scale, rev, plotHeatmap, nseq, metadata, length, label, image, coords, PatternHeatmap, PWMScanHeatmap, CoverageHeatmap, scale<-, nseq<-, metadata<-, label<-, image<-, coords<- ExportClasses: Heatmap Package: HelloRanges Exports: pair, distmode Package: HELP Exports: readSampleKey ExportMethods: calcGC, calcPrototype, calcTm, combineData, createWiggle, exprs2, exprs2<-, fuzzyMatches, getFeatures, getSamples, plotBins, plotChip, plotFeature, plotPairs, quantileNormalize, readDesign, readPairs Package: HEM Exports: am.tran, am.tran.half, base.ASE.Olig, base.error.Olig, base.error.Olig.quanOnly, base.PSE.Olig, boot.base.ASE.Olig, boot.base.error.Olig, boot.base.PSE.Olig, fixbound.predict.smooth.spline, hem, hem.eb.prior, hem.fdr, hem.null.no, hem.null.one, hem.null.two, hem.preproc, nonpar.error.Olig, nonpar.no.error.Olig, nonpar.rep.error.Olig, par.error.Olig, par.no.error.Olig, par.rep.error.Olig, permut, quant.normal, quant.normal2, remove.sig.genes Package: hiAnnotator Exports: cleanColname, doAnnotation, get2NearestFeature, getFeatureCounts, getFeatureCountsBig, getLowestDists, getNearestFeature, getRelevantCol, getSitesInFeature, getUCSCtable, getWindowLabel, makeChunks, makeGRanges, makeUCSCsession, plotdisFeature Package: HIBAG Exports: .onAttach Package: HiCBricks Exports: Create_many_Bricks, Brick_get_chrominfo, Brick_make_ranges, Brick_add_ranges, Brick_list_rangekeys, Brick_rangekey_exists, Brick_list_ranges_mcols, Brick_list_matrices, Brick_get_ranges, Brick_get_bintable, Brick_fetch_range_index, Brick_return_region_position, Brick_load_matrix, Brick_load_cis_matrix_till_distance, Brick_matrix_isdone, Brick_matrix_maxdist, Brick_matrix_exists, Brick_matrix_minmax, Brick_matrix_filename, Brick_get_values_by_distance, Brick_get_matrix_within_coords, Brick_get_matrix, Brick_fetch_row_vector, Brick_get_vector_values, Brick_list_matrix_mcols, Brick_get_matrix_mcols, Brick_local_score_differentiator, Brick_matrix_issparse, Brick_vizart_plot_heatmap, Brick_list_mcool_normalisations, Brick_mcool_normalisation_exists, Brick_matrix_dimensions, Create_many_Bricks_from_mcool, Brick_load_data_from_mcool, Brick_list_mcool_resolutions, BrickContainer_list_chromosomes, BrickContainer_list_resolutions, BrickContainer_list_output_directory, BrickContainer_list_experiment_name, BrickContainer_unlink_resolution, BrickContainer_change_output_directory, BrickContainer_change_experiment_name, BrickContainer_get_path_to_file, BrickContainer_list_files, Brick_call_compartments, Brick_get_entire_matrix, load_BrickContainer, Brick_export_to_sparse Package: HiCcompare Exports: KRnorm, MA_norm, MD.plot1, MD.plot2, SCN, cooler2bedpe, cooler2sparse, create.hic.table, filter_params, full2sparse, get_CNV, hic_compare, hic_diff, hic_loess, hic_simulate, hicpro2bedpe, make_InteractionSet, manhattan_plot, remove_centromere, sim.other.methods, sim_matrix, sparse2full, split_centromere, total_sum, visualize_pvals Package: hicrep Exports: MatToVec, depth.adj, get.scc, htrain, prep, smoothMat, vstran Package: hierGWAS Exports: cluster.snp, multisplit, test.hierarchy, compute.r2 Package: hierinf Exports: cluster_position, cluster_var, compute_r2, multisplit, test_hierarchy, test_only_hierarchy Package: HilbertCurve Exports: GenomicHilbertCurve, HilbertCurve, default_overlay, is_white, GenomicHilbertCurve, HilbertCurve ExportMethods: zoom, unzoom, hc_text, hc_segments, hc_segmented_points, hc_rect, hc_polygon, hc_points, hc_png, hc_offset, hc_normal_points, hc_map, hc_level, hc_layer, hc_centered_text ExportClasses: HilbertCurve, GenomicHilbertCurve Package: HilbertVis Exports: hilbertCurve, hilbertCurvePoint, plotHilbertCurve, shrinkVector, plotLongVector, makeWiggleVector, hilbertImage, makeRandomTestData, showHilbertImage Package: HilbertVisGUI Exports: simpleLinPlot, hilbertDisplay, hilbertDisplayThreeChannel, dotsapply Package: HiLDA Exports: hildaBarplot, hildaDiffPlot, hildaGlobalResult, hildaLocalResult, hildaPlotSignature, hildaReadMPFile, hildaRhat, hildaTest, pmBarplot, pmMultiBarplot, pmPlotSignature, pmgetSignature, visPMS ExportClasses: MutationFeatureData, EstimatedParameters Package: hipathia Exports: create_report, do_pca, do_wilcoxon, get_go_names, get_node_names, get_nodes_data, get_path_names, get_paths_data, get_pathways_annotations, get_pathways_list, get_pathways_summary, heatmap_plot, hhead, hipathia, load_pathways, mgi_from_sif, multiple_pca_plot, node_color, node_color_per_de, normalize_data, normalize_paths, paths_to_go_ancestor, pathway_comparison_plot, pca_plot, quantify_terms, save_results, top_pathways, translate_data, visualize_report Package: hiReadsProcessor Exports: addFeature, addListNameToReads, annotateSites, blatListedSet, blatSeqs, chunkize, clusterSites, crossOverCheck, decodeByBarcode, dereplicateReads, doRCtest, extractFeature, extractSeqs, findAndRemoveVector, findAndTrimSeq, findBarcodes, findIntegrations, findLTRs, findLinkers, findPrimers, findVector, getIntegrationSites, getSectorsForSamples, getSonicAbund, isuSites, otuSites, pairUpAlignments, pairwiseAlignSeqs, primerIDAlignSeqs, pslCols, pslToRangedObject, read.BAMasPSL, read.SeqFolder, read.blast8, read.psl, read.sampleInfo, read.seqsFromSector, removeReadsWithNs, replicateReads, sampleSummary, splitByBarcode, splitSeqsToFiles, startgfServer, trimSeqs, troubleshootLinkers, vpairwiseAlignSeqs, write.listedDNAStringSet, write.psl Package: HIREewas Exports: HIRE, riskCpGpattern Package: HiTC Exports: HTCexp, HTClist, binningC, exportC, export.my5C, importC, import.my5C, removeIntervals, setIntervalScale, CQC, intervalsDist, extractRegion, pca.hic, getPearsonMap, getExpectedCounts, normLGF, normICE, setGenomicFeatures, getAnnotatedRestrictionSites, getRestrictionFragmentsPerChromosome, discretize, directionalityIndex ExportMethods: intdata, intdata<-, id, y_intervals, y_intervals<-, x_intervals, x_intervals<-, xy_intervals, getCombinedIntervals, getCombinedContacts, forcePairwise, forceTriangular, isComplete, isPairwise, isBinned, isIntraChrom, divide, substract, mapC, summary, as.list, c, detail, show, plot, seqlevels, range, ranges, reduce, forceSymmetric, isTriangular, isSymmetric, normPerReads, normPerTrans, normPerExpected ExportClasses: HTCexp, HTClist Package: hmdbQuery Exports: HmdbEntry ExportMethods: tissues, store, diseases, biospecimens ExportClasses: HmdbEntry Package: HMMcopy Exports: wigsToRangedData, correctReadcount, plotBias, plotCorrection, wigToRangedData, wigToArray, rangedDataToWig, rangedDataToSeg, HMMsegment, plotSegments, plotParam, stateCols Package: hopach Exports: boot2fuzzy, bootplot, bootmedoids, boothopach, dplot, vdisscosangle, vdissabscosangle, vdisseuclid, vdissabseuclid, vdisscor, vdissabscor, distancematrix, distancevector, dissvector, dissmatrix, vectmatrix, correlationordering, improveordering, disseuclid, disscor, dissabscor, disscosangle, dissabscosangle, makeTree, hopach2tree, labelstomss, silcheck, msscheck, digits, cutdigits, cutzeros, nonzeros, msssplitcluster, mssnextlevel, orderelements, mssinitlevel, paircoll, collap, msscollap, mssmulticollap, mssrundown, msscomplete, newnextlevel, newsplitcluster, hopach, makeoutput, prune, is.hdist, hdist ExportMethods: show, [, coerce, as.matrix, as.hdist, as.vector, length ExportClasses: hdist Package: HPAanalyze Exports: hpaDownload, hpaExport, hpaListParam, hpaSubset, hpaVis, hpaVisPatho, hpaVisSubcell, hpaVisTissue, hpaXml, hpaXmlAntibody, hpaXmlGet, hpaXmlProtClass, hpaXmlTissueExpr, hpaXmlTissueExprSum Package: hpar Exports: getHpaVersion, getHpaDate, getHpaEnsembl, getHpa, allHparData, getHparOptions, setHparOptions Package: HTqPCR Exports: changeCtLayout, clusterCt, filterCategory, filterCtData, getCt, getCtHistory, heatmapSig, limmaCtData, mannwhitneyCtData, n.samples, n.wells, normalizeCtData, plotCtArray, plotCtBoxes, plotCtCategory, plotCtCor, plotCtDensity, plotCtHeatmap, plotCtHistogram, plotCtOverview, plotCtPCA, plotCtReps, plotCtRQ, plotCtScatter, plotCtSignificance, plotCtVariation, plotCVBoxes, plotCtLines, plotCtCard, readCtData, setCategory, setCt<-, setCtHistory<-, ttestCtData, plotCtPairs ExportMethods: [, exprs, exprs<-, featureCategory, featureCategory<-, featureClass, featureClass<-, featureNames, featureNames<-, featurePos, featurePos<-, featureType, featureType<-, flag, flag<-, sampleNames, sampleNames<-, show, summary ExportClasses: qPCRset Package: HTSeqGenie Exports: FastQStreamer.getReads, FastQStreamer.init, FastQStreamer.release, TP53GenomicFeatures, alignReads, analyzeVariants, annotateVariants, bamCountUniqueReads, buildConfig, buildGenomicFeaturesFromTxDb, buildTP53FastaGenome, calculateCoverage, calculateTargetLengths, checkConfig, checkGATKJar, checkPicardJar, computeBamStats, computeCoverage, countGenomicFeatures, countGenomicFeaturesChunk, detectAdapterContam, detectQualityInFASTQFile, detectRRNA, filterByLength, filterQuality, findVariantFile, gatk, getBams, getChunkDirs, getConfig, getConfig.integer, getConfig.logical, getConfig.numeric, getConfig.vector, getEndNumber, getMemoryUsage, getNumberOfReadsInFASTQFile, getNumericVectorDataFromFile, getObjectFilename, getPackageFile, getRRNAIds, getTabDataFromFile, getTraceback, hashCoverage, hashVariants, hashVector, initDirs, initLog, initLogger, initPipelineFromConfig, initPipelineFromSaveDir, isAboveQualityThresh, isAdapter, isConfig, listIterator.init, listIterator.next, loadConfig, logdebug, logerror, loginfo, logwarn, makeDir, markDuplicates, markDups, mergeAlignReads, mergeCoverage, mergeLanes, mergePreprocessReads, mergeSummaryAlignment, parseDCF, parseSummaries, plotDF, preprocessReads, processChunks, readInputFiles, readRNASeqEnds, realignIndels, relativeBarPlot, removeChunkDir, resource, rpkm, runAlignment, runPipeline, runPipelineConfig, runPreprocessReads, safe.yield, safeExecute, safeGetObject, safeUnlink, saveWithID, sclapply, setUpDirs, setupTestFramework, statCountFeatures, traceMem, trimReads, trimTailsByQuality, truncateReads, tryKeepTraceback, updateConfig, vcfStat, wrap.callVariants, writeAudit, writeConfig, writeFastQFiles, writeFeatureCountsHTML, writeGenomicFeaturesReport, writePreprocessAlignReport, writeSummary, writeVCF Package: HTSFilter Exports: HTSBasicFilter, HTSFilter, normalizeData ExportMethods: HTSFilter Package: HumanTranscriptomeCompendium Exports: addRD, ca43k, get_ds4841, htx_app, htx_load, htx_query_by_study_accession, htx_query_by_text, load_bigrnaFiles, load_experTable, load_studTable, path_doc4842, procExpToGene, tx2gene_gencode27 Package: HybridMTest Exports: hybrid.test, row.oneway.anova, row.kruskal.wallis, row.kgrp.shapiro, row.kgrp.shapiro, row.pearson, row.spearman, row.slr.shapiro, grenander.ebp Package: hypeR Exports: ggempty, ggeplot, ggvenn, hyp, hyp_dots, hyp_emap, hyp_hmap, hyp_show, hyp_to_excel, hyp_to_rmd, hyp_to_table, hypeR, hyperdb_fetch, hyperdb_info, msigdb_download_all, msigdb_download_one, msigdb_fetch, msigdb_info, multihyp, pvector, rgsets Package: hyperdraw ExportMethods: graphBPH, plot, graphLayout, edgeDataDefaults<-, edgeData<-, nodeDataDefaults<-, nodeData<-, graphDataDefaults<-, graphData<- ExportClasses: graphBPH, RagraphBPH Package: hypergraph Exports: kCoresHypergraph, vCoverHypergraph, Hypergraph, Hyperedge, DirectedHyperedge, l2hel ExportMethods: nodes, label, label<-, show, toUndirected, head, tail, hyperedges, numNodes, inciMat, inciMat2HG, initialize, toGraphNEL, hyperedgeLabels ExportClasses: Hypergraph, Hyperedge, DirectedHyperedge Package: iASeq Exports: ASErawfit, iASeqmotif, singleEMfit, plotBIC, plotMotif Package: iasva Exports: fast_iasva, find_markers, iasva, study_R2 Package: iBBiG Exports: iBBiG, makeArtificial, makeSimDesignMat ExportMethods: plot, show, summary, RowScorexNumber, Clusterscores, Seeddata, Parameters, RowxNumber, NumberxCol, Number, info, analyzeClust, JIdist ExportClasses: iBBiG Package: iBMQ Exports: calculateThreshold, eqtlClassifier, eqtlFinder, eqtlMcmc, hotspotFinder Package: iCARE Exports: computeAbsoluteRisk, computeAbsoluteRiskSplitInterval, ModelValidation, plotModelValidation Package: Icens Exports: Bisect, BVcliques, BVclmat, BVmacprod, BVsupport, EM, EMICM, EMICMmac, Intersection, ISDM, Maclist, Macmat, MLEintvl, PGM, Plotboxes, PMGA, rescaleP, Subset, VEM, VEMICMmac Package: icetea Exports: sampleInfo<-, annotateTSS, demultiplexFASTQ, detectDiffTSS, detectTSS, exampleCSobject, filterDuplicates, fitDiffTSS, getGeneCounts, getNormFactors, mapCaps, newCapSet, plotReadStats, plotTSSprecision, sampleInfo, splitBAM_byIndex, splitBAM_byRepindex ExportMethods: sampleInfo, plotTSSprecision, plotReadStats, getNormFactors, getGeneCounts, fitDiffTSS, filterDuplicates, exportTSS, detectTSS, detectDiffTSS, demultiplexFASTQ, sampleInfo<- Package: iCheck Exports: boxPlots, densityPlots, genExprSet, genSimData.BayesNormal, getPCAFunc, glmWrapper, lkhrWrapper, lmFitPaired, lmFitWrapper, LumiBatch2Table, pca2DPlot, pca3DPlot, plotCurves, plotQCCurves, plotSamplep95p05, quantilePlot, R2PlotFunc, scatterPlots, sortExpressionSet Package: iChip Exports: iChip1, iChip2, enrichreg, lmtstat Package: iClusterPlus Exports: compute.pod, plotiCluster, iCluster, iCluster2, tune.iCluster2, iClusterPlus, tune.iClusterPlus, plotHeatmap, getBIC, getDevR, getClusters, CNregions, iClusterBayes, tune.iClusterBayes, plotHMBayes, iManual Package: iCNV Exports: bambaf_from_vcf, bed_generator, get_array_input, iCNV_detection, icnv_output_to_gb, output_list, plotHMMscore, plot_intensity, plotindi Package: iCOBRA Exports: corr<-, deviation<-, facetted<-, fdrnbr<-, fdrnbrcurve<-, fdrtpr<-, fdrtprcurve<-, fpc<-, fpr<-, fsrnbr<-, fsrnbrcurve<-, maxsplit<-, onlyshared<-, overlap<-, padj<-, plotcolors<-, pval<-, roc<-, scatter<-, score<-, splv<-, sval<-, tpr<-, truth<-, COBRAData, COBRAData_from_text, COBRAData_to_text, COBRAPerformance, COBRAPlot, COBRAapp, basemethods, calculate_adjp, calculate_performance, coerce, corr, deviation, facetted, fdrnbr, fdrnbrcurve, fdrtpr, fdrtprcurve, fpc, fpr, fsrnbr, fsrnbrcurve, maxsplit, onlyshared, overlap, padj, plot_corr, plot_deviation, plot_fdrnbrcurve, plot_fdrtprcurve, plot_fpc, plot_fpr, plot_fsrnbrcurve, plot_overlap, plot_roc, plot_scatter, plot_tpr, plot_upset, plotcolors, prepare_data_for_plot, pval, reorder_levels, roc, scatter, score, splv, stratiflevels, sval, tpr, truth, update_cobradata, update_cobraperformance ExportMethods: truth, tpr, sval, stratiflevels, splv, score, scatter, roc, pval, plotcolors, padj, overlap, onlyshared, maxsplit, fsrnbrcurve, fsrnbr, fpr, fpc, fdrtprcurve, fdrtpr, fdrnbrcurve, fdrnbr, facetted, deviation, corr, basemethods, truth<-, tpr<-, sval<-, splv<-, score<-, scatter<-, roc<-, pval<-, plotcolors<-, padj<-, overlap<-, onlyshared<-, maxsplit<-, fsrnbrcurve<-, fsrnbr<-, fpc<-, fdrtprcurve<-, fdrtpr<-, fdrnbrcurve<-, fdrnbr<-, facetted<-, deviation<-, corr<-, [ ExportClasses: COBRAPlot, COBRAPerformance, COBRAData Package: ideal Exports: deseqresult2DEgenes, deseqresult2tbl, ggplotCounts, goseqTable, ideal, plot_ma, plot_volcano, read_gmt, sepguesser, sig_heatmap, wrapup_for_iSEE Package: IdeoViz Exports: avgByBin, getBins, getIdeo, plotChromValuePair, plotOnIdeo Package: idiogram Exports: .usedChromExprs, .rwb ExportClasses: cytoband Package: idr2d Exports: calculate_midpoint_distance1d, calculate_midpoint_distance2d, calculate_relative_overlap1d, calculate_relative_overlap2d, determine_anchor_overlap, draw_idr_distribution_histogram, draw_rank_idr_scatterplot, draw_value_idr_scatterplot, establish_bijection, establish_bijection1d, establish_bijection2d, establish_overlap1d, establish_overlap2d, estimate_idr, estimate_idr1d, estimate_idr2d, estimate_idr2d_hic, parse_hic_file, preprocess, remove_nonstandard_chromosomes1d, remove_nonstandard_chromosomes2d Package: iGC Exports: create_gene_cna, create_gene_exp, create_sample_desc, direct_gene_cna, find_cna_driven_gene Package: IgGeneUsage Exports: DGU, LOO Package: igvR Exports: DataFrameAnnotationTrack, DataFrameQuantitativeTrack, GRangesAnnotationTrack, GRangesQuantitativeTrack, GenomicAlignmentTrack, QuantitativeTrack, Track, UCSCBedAnnotationTrack, UCSCBedGraphQuantitativeTrack, VariantTrack, igvR ExportMethods: trackSize, trackInfo, showGenomicRegion, setTrackClickFunction, setGenome, saveToSVG, removeTracksByName, ping, getTrackNames, getSupportedGenomes, getGenomicRegion, enableMotifLogoPopups, displayTrack ExportClasses: igvR, igvAnnotationTrack, VariantTrack, UCSCBedGraphQuantitativeTrack, UCSCBedAnnotationTrack, Track, QuantitativeTrack, GenomicAlignmentTrack, GRangesQuantitativeTrack, GRangesAnnotationTrack, DataFrameQuantitativeTrack, DataFrameAnnotationTrack Package: IHW Exports: get_bh_threshold, groups_by_filter, ihw ExportMethods: weights, weighted_pvalues, thresholds, show, rejections, rejected_hypotheses, regularization_term, pvalues, plot, nrow, nfolds, nbins, m_groups, groups_factor, covariates, covariate_type, as.data.frame, alpha, adj_pvalues Package: illuminaio Exports: readBGX, readBPM, readIDAT 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: IMAS Exports: ClinicAnalysis, CompGroupAlt, ExonsCluster, MEsQTLFinder, RatioFromReads, ASvisualization, SplicingReads Package: Imetagene Exports: shiny_metagene Package: IMMAN Exports: IMMAN Package: ImmuneSpaceR Exports: CreateConnection, ISpalette, check_netrc, interactive_netrc, loadConnection, saveConnection, template_IS, theme_IS, write_netrc Package: immunoClust ExportMethods: show, summary, plot, splom ExportClasses: immunoClust Package: IMPCdata Exports: getPhenCenters, printPhenCenters, getPipelines, printPipelines, getParameters, printParameters, getProcedures, printProcedures, getGenes, printGenes, getAlleles, printAlleles, getStrains, printStrains, getName, getZygosities, getIMPCTable, getIMPCDataset Package: ImpulseDE Exports: calc_impulse, impulse_DE, plot_impulse Package: ImpulseDE2 Exports: computeNormConst, fitSigmoidModels, get_boolCaseCtrl, get_dfAnnotationProc, get_lsModelFits, get_matCountDataProc, get_scaNProc, get_scaQThres, get_strReport, get_vecAllIDs, get_vecConfounders, get_vecDispersions, get_vecSizeFactors, plotGenes, plotHeatmap, runImpulseDE2, simulateDataSetImpulseDE2, updateDEAnalysis, writeReportToFile ExportMethods: names, [[, $ Package: impute Exports: impute.knn Package: INDEED Exports: network_display, non_partial_cor, partial_cor, select_rho_partial Package: infercnv Exports: CreateInfercnvObject, add_to_seurat, apply_median_filtering, filterHighPNormals, inferCNVBayesNet, plot_cnv, plot_per_group, run, sample_object ExportClasses: infercnv, MCMC_inferCNV Package: InPAS Exports: coverageFromBedGraph, coverageRate, CPsites, filterRes, fisher.exact.test, getUTR3eSet, inPAS, limmaAnalyze, prepare4GSEA, singleGroupAnalyze, singleSampleAnalyze, testUsage, utr3Annotation, utr3UsageEstimation, usage4plot ExportMethods: $, $<- ExportClasses: UTR3eSet Package: INPower Exports: INPower Package: INSPEcT Exports: newINSPEcT, runINSPEcTGUI, compareSteadyNoNascent, quantifyExpressionsFromBAMs, quantifyExpressionsFromTrCounts, quantifyExpressionsFromTrAbundance ExportMethods: [, AIC, calculateDelta, calculateTau, chisqmodel, chisqtest, combine, compareSteady, computeConfidenceIntervals, correlationPlot, degradation, dim, featureNames, featureNames<-, geneClass, getModel, getModel<-, inHeatmap, labeledSF, logLik, makeModelRates, makeSimDataset, makeSimModel, makeOscillatorySimModel, modelingParams, modelingParams<-, modelRates, modelRatesNF, modelSelection, modelSelection<-, nGenes, nTpts, plotGene, plotMA, processing, processingDelay, ratePvals, ratesFirstGuess, ratesFirstGuessVar, removeModel, rocCurve, rocThresholds, sfPlot, show, split, synthesis, tpts, viewModelRates, viewConfidenceIntervals ExportClasses: INSPEcT, INSPEcT_model, INSPEcT_diffsteady Package: InTAD Exports: combineInTAD, filterGeneExpr, findCorrelation, geneCoords, loadSigInTAD, newSigInTAD, plotCorAcrossRef, plotCorrelation, sigCoords, signals ExportMethods: signals, sigCoords, geneCoords, exprs ExportClasses: InTADSig Package: intansv Exports: methodsMerge, plotChromosome, plotRegion, readBreakDancer, readCnvnator, readDelly, readPindel, readSvseq, svAnnotation, readLumpy, readSoftSearch Package: InteractionSet Exports: makeGInteractionsFromGRangesPairs ExportMethods: GInteractions, anchors, anchorIds, regions, reduceRegions, swapAnchors, regions<-, replaceRegions<-, appendRegions<-, anchorIds<-, pairs, findOverlaps, countOverlaps, InteractionSet, interactions, interactions<-, pairdist, intrachr, linearize, linkOverlaps, boundingBox, ContactMatrix, as.matrix<-, inflate, deflate ExportClasses: GInteractions, StrictGInteractions, ReverseStrictGInteractions, InteractionSet, ContactMatrix Package: interactiveDisplay Exports: display ExportMethods: altgr, simplenet, bicgo, gridtweak, gridsvgjs, display Package: interactiveDisplayBase Exports: .runApp, display ExportMethods: display Package: IntEREst Exports: interest, interest.sequential, InterestResult, getAnnotation, addAnnotation, scaledRetention, referencePrepare, readInterestResults, subInterestResult, mergeInterestResult, u12NbIndex, u12Index, exactTestInterest, glmInterest, qlfInterest, treatInterest, u12BoxplotNb, u12DensityPlot, u12DensityPlotIntron, lfc, getRepeatTable, u12Boxplot, annotateU12, intexIndex, buildSsTypePwms, updateRowDataCol, counts.InterestResults, plot.InterestResult, intexBoxplot, DEXSeqIntEREst, unionRefTr, interestResultIntEx, deseqInterest, psi, applyOverlap ExportMethods: counts, plot, boxplot Package: InterMineR Exports: convertToGRanges, convertToGeneAnswers, convertToRangedSummarizedExperiment, doEnrichment, getDatasets, getGeneIds, getModel, getRelease, getTemplateQuery, getTemplates, getVersion, getWidgets, initInterMine, listDatasets, listMines, newQuery, runQuery, setConstraints, setQuery, simplifyResult ExportMethods: getWhere, getOrderBy, getSelect, getDescription, getName, summary, runQuery ExportClasses: InterMineR Package: IntramiRExploreR Exports: Gene_Visualisation, GetGOS_ALL, Visualisation, extract_HostGene, extract_intragenic_miR, genes_Stat, miRTargets_Stat 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: IONiseR Exports: channelActivityPlot, channelHeatmap, fast5toFastq, layoutPlot, plotActiveChannels, plotBaseProductionRate, plotCurrentByTime, plotEventRate, plotKmerFrequencyCorrelation, plotReadAccumulation, plotReadCategoryCounts, plotReadCategoryQuals, plotReadTypeProduction, readFast5Log, readFast5Summary ExportMethods: readInfo, length, fastqTemplate, fastqComplement, fastq2D, fastq, eventData, baseCalled, [ ExportClasses: Fast5Summary Package: iPAC Exports: ClusterFind, get.AASeq, get.AlignedPositions, get.Positions, get.SingleLetterCode, nmc, Plot.Protein.Linear, get.Remapped.Order Package: ipdDb Exports: loadHlaData, loadKirData ExportMethods: select, keytypes, keys, getStructure, getReference, getLoci, getClosestComplete, getAlleles, columns Package: IPO Exports: attachList, calcPPS, calculateXcmsSet, combineParams, createModel, decode, decodeAll, encode, getBbdParameter, getCcdParameter, getDefaultRetGroupStartingParams, getDefaultXcmsSetStartingParams, getRGTVValues, findIsotopes.CAMERA, findIsotopes.IPO, optimizeRetGroup, optimizeXcmsSet, toMatrix, typeCastParams, writeRScript, writeParamsTable Package: IPPD Exports: sweepline, analyzeLCMS, read.mzXML, new.mzXML ExportMethods: show, getPeaklist, fitModelParameters, threshold, visualize ExportClasses: peaklist, modelfit Package: IRanges Exports: as.data.frame.IPosRanges, as.data.frame.IPos, diff.AtomicList, window<-.Vector, window<-.vector, window<-.factor, multisplit, solveUserSEW0, IRanges, solveUserSEW, successiveIRanges, slidingIRanges, breakInChunks, whichAsIRanges, asNormalIRanges, rangeComparisonCodeToLetter, IPos, NCList, NCLists, H2LGrouping, Dups, PartitioningByEnd, PartitioningByWidth, PartitioningMap, RangedData, RangedSelection, RangesList, IRangesList, RleViewsList, %over%, %within%, %outside%, %pover%, %pwithin%, %poutside%, mergeByOverlaps, findOverlapPairs, MaskCollection.show_frame, Mask, read.gapMask, read.agpMask, read.liftMask, read.rmMask, read.trfMask, successiveViews, slidingViews, LogicalList, IntegerList, NumericList, ComplexList, CharacterList, RawList, RleList, FactorList, DataFrameList, SplitDataFrameList, ManyToOneGrouping, ManyToManyGrouping, regroup, heads, tails, selectNearest, INCOMPATIBLE_ARANGES_MSG, extractListFragments, equisplit, ranges, rglist, showAsCell, mstack, mid, isNormal, whichFirstNotNormal, subject, ranges<-, Views, trim, subviews, viewApply, viewMins, viewMaxs, viewSums, viewMeans, viewWhichMins, viewWhichMaxs, viewRangeMins, viewRangeMaxs, nobj, grouplengths, members, vmembers, togroup, togrouplength, high2low, low2high, grouprank, togrouprank, mapOrder, findRange, splitRanges, extractList, columnMetadata, columnMetadata<-, universe, universe<-, space, nir_list, desc, desc<-, maskedwidth, maskedratio, collapse, findOverlaps, countOverlaps, overlapsAny, subsetByOverlaps, overlapsRanges, poverlaps, windows, narrow, update_ranges, shift, resize, flank, reflect, promoters, restrict, threebands, reduce, gaps, disjoin, isDisjoint, disjointBins, reverse, coverage, cvg, slice, punion, pintersect, psetdiff, pgap, precede, follow, nearest, distance, distanceToNearest, tile, slidingWindows, ifelse2 ExportMethods: ranges, rglist, runsum, runmean, runwtsum, runq, showAsCell, mstack, mid, isNormal, whichFirstNotNormal, subject, ranges<-, Views, trim, subviews, viewApply, viewMins, viewMaxs, viewSums, viewMeans, viewWhichMins, viewWhichMaxs, viewRangeMins, viewRangeMaxs, nobj, grouplengths, members, vmembers, togroup, togrouplength, high2low, low2high, grouprank, togrouprank, mapOrder, findRange, splitRanges, extractList, columnMetadata, columnMetadata<-, universe, universe<-, space, nir_list, desc, desc<-, maskedwidth, maskedratio, collapse, findOverlaps, countOverlaps, overlapsAny, subsetByOverlaps, overlapsRanges, poverlaps, windows, narrow, update_ranges, shift, resize, flank, reflect, promoters, restrict, threebands, reduce, gaps, disjoin, isDisjoint, disjointBins, reverse, coverage, cvg, slice, punion, pintersect, psetdiff, pgap, precede, follow, nearest, distance, distanceToNearest, tile, slidingWindows, ifelse2, length, length<-, names, names<-, nrow, NROW, ncol, NCOL, dim, rownames, rownames<-, colnames, colnames<-, dimnames, dimnames<-, [, [<-, [[, [[<-, as.vector, as.integer, as.character, as.factor, as.matrix, as.data.frame, as.list, coerce, show, match, duplicated, unique, anyDuplicated, is.unsorted, order, Ops, Math, Math2, Summary, Complex, summary, drop, start, start<-, end, end<-, width, width<-, pos, min, max, range, which.max, which.min, diff, mean, var, cov, cor, sd, median, quantile, mad, IQR, smoothEnds, runmed, window<-, transform, nchar, chartr, tolower, toupper, sub, gsub, unlist, stack, split<-, unsplit, relist, append, !, which, merge, is.na, by, cbind, rbind, lapply, pmax, pmin, pmax.int, pmin.int, paste, table, tapply, union, intersect, setdiff, updateObject, bindROWS, extractROWS, replaceROWS, getListElement, parallelSlotNames, values, values<-, classNameForDisplay, from, to, nLnode, nRnode, pcompare, pcompareRecursively, selfmatch, runLength, runValue<-, elementNROWS, isEmpty, relistToClass, revElements, as.env, active, active<- ExportClasses: DataFrameList, DFrameList, SimpleDataFrameList, SimpleDFrameList, SplitDataFrameList, SplitDFrameList, SimpleSplitDataFrameList, SimpleSplitDFrameList, AtomicList, SimpleAtomicList, LogicalList, SimpleLogicalList, IntegerList, SimpleIntegerList, NumericList, SimpleNumericList, ComplexList, SimpleComplexList, CharacterList, SimpleCharacterList, RawList, SimpleRawList, RleList, SimpleRleList, FactorList, SimpleFactorList, Ranges, IntegerRanges, Pos, RangesList, SimpleRangesList, IntegerRangesList, SimpleIntegerRangesList, PosList, SimplePosList, IPosRanges, IRanges, NormalIRanges, IPos, UnstitchedIPos, StitchedIPos, Grouping, ManyToOneGrouping, ManyToManyGrouping, H2LGrouping, Dups, GroupingRanges, GroupingIRanges, Partitioning, PartitioningByEnd, PartitioningByWidth, PartitioningMap, Views, RleViews, SimpleGrouping, SimpleManyToOneGrouping, BaseManyToManyGrouping, SimpleManyToManyGrouping, IRangesList, SimpleIRangesList, NormalIRangesList, SimpleNormalIRangesList, IPosList, SimpleIPosList, ViewsList, SimpleViewsList, RleViewsList, SimpleRleViewsList, RangedSelection, MaskCollection, CompressedList, CompressedDataFrameList, CompressedDFrameList, CompressedSplitDataFrameList, CompressedSplitDFrameList, CompressedAtomicList, CompressedLogicalList, CompressedIntegerList, CompressedNumericList, CompressedComplexList, CompressedCharacterList, CompressedRawList, CompressedRleList, CompressedFactorList, CompressedGrouping, CompressedManyToOneGrouping, CompressedManyToManyGrouping, CompressedRangesList, CompressedPosList, CompressedIntegerRangesList, CompressedIRangesList, CompressedNormalIRangesList, CompressedIPosList, RangedData, NCList, NCLists, IntegerRanges_OR_missing Package: iSeq Exports: iSeq1, iSeq2, peakreg, mergetag, plotreg Package: isobar Exports: IBSpectraTypes ExportMethods: as.data.frame ExportClasses: IBSpectra, ProteinGroup Package: IsoCorrectoR Exports: IsoCorrection Package: IsoCorrectoRGUI Exports: GetGUIstatus, IsoCorrectionGUI Package: IsoformSwitchAnalyzeR Exports: createSwitchAnalyzeRlist, subsetSwitchAnalyzeRlist, importCufflinksFiles, importGTF, importIsoformExpression, importRdata, preFilter, isoformSwitchTestDRIMSeq, isoformSwitchTestDEXSeq, extractSwitchSummary, extractSwitchOverlap, extractTopSwitches, CDSSet, getCDS, extractSequence, analyzeORF, analyzeCPAT, analyzeCPC2, analyzePFAM, analyzeSignalP, analyzeNetSurfP2, analyzeIUPred2A, analyzeAlternativeSplicing, analyzeIntronRetention, extractSplicingSummary, extractSplicingEnrichment, extractSplicingEnrichmentComparison, extractSplicingGenomeWide, analyzeSwitchConsequences, extractConsequenceSummary, extractConsequenceEnrichment, extractConsequenceEnrichmentComparison, extractConsequenceGenomeWide, extractGenomeWideAnalysis, switchPlotTranscript, switchPlotGeneExp, switchPlotIsoExp, switchPlotIsoUsage, switchPlot, switchPlotTopSwitches, isoformSwitchAnalysisPart1, isoformSwitchAnalysisPart2, isoformSwitchAnalysisCombined, isoformToGeneExp, isoformToIsoformFraction ExportClasses: switchAnalyzeRlist Package: IsoGeneGUI Exports: IsoGeneGUI, IsoGeneGUIHelp Package: ISoLDE Exports: readRawInput, readNormInput, readTarget, filterT, isolde_test Package: isomiRs Exports: IsomirDataSeqFromFiles, IsomirDataSeqFromRawData, findTargets, isoAnnotate, isoCounts, isoDE, isoNetwork, isoNorm, isoPLSDA, isoPLSDAplot, isoPlot, isoPlotNet, isoPlotPosition, isoTop, mirna2targetscan, updateIsomirDataSeq ExportMethods: isoSelect, design<-, design, counts<-, counts ExportClasses: IsomirDataSeq Package: ITALICS Exports: ITALICS, analyseCGH, getQuartet, getResidu, getCorrection, getEffet, getConfDat, getModel, readQuartetCopyNb, getSnpInfo, fromSnpToQuartet, fromQuartetToSnp, addInfo, trainITALICS Package: iterativeBMA Exports: BssWssFast, bma.predict, brier.score, imageplot.iterate.bma, iterateBMAglm.train, iterateBMAglm.train.predict, iterateBMAglm.train.predict.test, iterateBMAglm.wrapper Package: iterativeBMAsurv Exports: assignRiskGroup, crossVal, crossVal.final.calc, crossVal.fold, crossVal.init, crossVal.run, crossVal.tabulate, imageplot.bma.mod, imageplot.iterate.bma.surv, iterateBMAinit, iterateBMAsurv.train, iterateBMAsurv.train.predict.assess, iterateBMAsurv.train.wrapper, predictBicSurv, predictiveAssessCategory, printTopGenes, singleGeneCoxph Package: iterClust Exports: iterClust, featureSelect, coreClust, clustEval, clustHetero, obsEval, obsOutlier Package: iteremoval Exports: feature_hist, feature_prevalence, feature_removal, feature_screen, funcOrExp, ggiteration_trace, linear_combine, min_max, ones, reciprocal_colSums Package: IVAS Exports: chrseparate, findAlternative, findOversnp, saveBplot, sQTLsFinder, Splicingfinder, CalSigSNP, RatioFromFPKM, calSignificant, MsqtlFinder, sqtlfinder Package: ivygapSE Exports: designOverview, exprByType, getRefLimma, ivyGlimpse, makeGeneSets, nomenclat, subBlockDetails, tumorDetails, vocab Package: IWTomics Exports: IWTomicsData, nRegions, nFeatures, lengthRegions, lengthFeatures, resolution, regions, features, idRegions, idFeatures, nameRegions, nameFeatures, alignment, smooth, testInput, nTests, idRegionsTest, idFeaturesTest, adjusted_pval, IWTomicsTest, plotTest, plotSummary ExportMethods: IWTomicsData, nRegions, nFeatures, lengthRegions, lengthFeatures, resolution, regions, features, idRegions, idFeatures, nameRegions, nameFeatures, alignment, smooth, testInput, nTests, idRegionsTest, idFeaturesTest, adjusted_pval, show, dim, [, c, merge, rbind, cbind, plot, metadata ExportClasses: IWTomicsData Package: joda Exports: differential.probs, regulation.scores, deregulation.scores, deregulation.p.values Package: JunctionSeq Exports: runJunctionSeqAnalyses, writeCompleteResults, buildAllPlots, readJunctionSeqCounts, estimateJunctionSeqDispersions, testForDiffUsage, estimateEffectSizes, estimateJunctionSeqSizeFactors, fitJunctionSeqDispersionFunction, readAnnotationData, plotMA, plotDispEsts, buildAllPlotsForGene, plotJunctionSeqResultsForGene, writeSizeFactors, writeExprBedTrack, writeSigBedTrack, JUNCTIONSEQ.DEFAULT.COLOR.LIST, setJunctionSeqCompiledSourcePackage ExportClasses: JunctionSeqCountSet Package: karyoploteR Exports: addGeneNames, autotrack, colByChr, colByRegion, colByValue, darker, filterParams, findIntersections, getChromosomeNamesBoundingBox, getColorSchemas, getCytobandColors, getCytobands, getDataPanelBoundingBox, getDefaultPlotParams, getMainTitleBoundingBox, getTextSize, getVariantsColors, horizonColors, is.color, kpAbline, kpAddBaseNumbers, kpAddChromosomeNames, kpAddChromosomeSeparators, kpAddCytobandLabels, kpAddCytobands, kpAddCytobandsAsLine, kpAddLabels, kpAddMainTitle, kpArea, kpArrows, kpAxis, kpBars, kpDataBackground, kpHeatmap, kpLines, kpPlotBAMCoverage, kpPlotBAMDensity, kpPlotBigWig, kpPlotCoverage, kpPlotDensity, kpPlotGenes, kpPlotHorizon, kpPlotLinks, kpPlotLoess, kpPlotManhattan, kpPlotMarkers, kpPlotNames, kpPlotRainfall, kpPlotRegions, kpPlotRibbon, kpPlotTranscripts, kpPoints, kpPolygon, kpRect, kpSegments, kpText, lighter, makeGenesDataFromTxDb, mergeTranscripts, plotDefaultPlotParams, plotKaryotype, plotPalettes, prepareParameters2, prepareParameters4, processClipping, transparent Package: KCsmart Exports: calcSpm, calcSpmCollection, getSigSegments, findSigLevelTrad, findSigLevelFdr, plotScaleSpace, idPoints, compareSpmCollection, getSigRegionsCompKC ExportMethods: plot, write.table, initialize, show, [[, [, [[<- ExportClasses: samplePointMatrix, sigSegments, spmCollection, compKc, compKcSigRegions Package: kebabs Exports: DNAVector, RNAVector, AAVector, genRandBioSeqs, annotationMetadata, annotationMetadata<-, annotationCharset, positionMetadata, positionMetadata<-, spectrumKernel, mismatchKernel, motifKernel, gappyPairKernel, linearKernel, symmetricPairKernel, getKernelMatrix, getExRep, getExRepQuadratic, getFeatureWeights, linWeight, expWeight, gaussWeight, swdWeight, getSVMSlotValue, seqKernelAsChar, computeROCandAUC, evaluatePrediction, showAnnotatedSeq, kebabsDemo, kebabsCollectInfo ExportMethods: kbsvm, predict, show, kernelParameters, as.KernelMatrix, getPredictionProfile, plot, profiles, baselines, sequences, featureWeights, featureWeights<-, modelOffset, modelOffset<-, cvResult, cvResult<-, modelSelResult, modelSelResult<-, svmModel, svmModel<-, probabilityModel, probabilityModel<-, gridRows, gridColumns, gridErrors, performance, selGridRow, selGridCol, fullModel, length, width, names, names<-, performCrossValidation, auc, auc<-, tpr, tpr<-, fpr, fpr<-, trainSVM, predictSVM, SVindex, heatmap, folds, isUserDefined, getFeatureSpaceDimension, getPredProfMixture ExportClasses: DNAVector, RNAVector, AAVector, SequenceKernel Package: KEGGgraph Exports: subGraph, nodes, edges, edgeData, nodeData, ugraph, numEdges, numNodes, plot, subGraph, inEdges, nodes<-, translateKEGGID2GeneID, translateGeneID2KEGGID, translateKEGGgraph, graphDensity, mergeGraphs, mergeKEGGgraphs, randomSubGraph, subKEGGgraph, subGraphByNodeType, getRgraphvizEdgeNames, getKEGGnodeData, getKEGGedgeData, neighborhood, queryKEGGsubgraph, getKGMLurl, retrieveKGML, kgmlFileName2PathwayName, parseKGML, KEGGpathway2Graph, parseKGML2Graph, KEGGpathway2reactionGraph, parseKGML2DataFrame, parseKGMLexpandMaps, splitKEGGgroup, expandKEGGPathway, parsePathwayInfo, parseEntry, parseRelation, parseReaction, getEntryID, pvalue2asterisk, getNamedElement, isHomoList, plotKEGGgraph, KEGGgraphLegend ExportMethods: getDisplayName, getEntryID, getKEGGID, getKEGGgeneLink, getType, getName, getSubtype, getValue, getTitle, getComponent, getPathwayInfo, getReactions, subtypeDisplay, getSubstrate, getProduct, show ExportClasses: KEGGEdge, KEGGGroup, KEGGNode, KEGGPathwayInfo, KEGGReaction, KEGGEdgeSubType, KEGGGraphics, KEGGPathway Package: KEGGlincs Exports: KEGG_lincs, KL_compare, add_edge_data, cyto_vis, edge_mapping_info, expand_KEGG_edges, expand_KEGG_mappings, generate_mappings, get_KGML, get_fisher_info, get_graph_object, keggerize_edges, node_mapping_info, overlap_info, path_genes_by_cell_type, refine_mappings, tidy_edge, toCytoscape Package: keggorthology Exports: getKOprobes, indRender, keggDF2graph, getKOtags Package: KEGGprofile Exports: col_by_value, convertId, download_KEGGfile, download_latest_pathway, find_enriched_pathway, newIdMatrix, parse_XMLfile, plot_pathway, plot_pathway_cor, plot_pathway_overall, plot_profile Package: KEGGREST Exports: keggInfo, keggList, listDatabases, keggFind, keggGet, keggConv, keggLink, mark.pathway.by.objects, color.pathway.by.objects Package: kimod Exports: DiStatis, Inertia.RV, RV, Euclid.Im, Inertia.comp, Compromise.Coords, Compromise.Matrix, RQO, Trajectories, Ratios.Boot, Comparisions.Boot, Elipses.Boot, Stability.Boot, QRO.Boot, EigValues.Boot, Inertia.Boot, SortList, ProyGroups, Groups, Coord.Select, Table.Select, List.Selec.Var, List.Selec.Est ExportMethods: summary, print, TrajPlot, SelectVar, RVPlot, PanelPlot, GroupProj, CompPlot, Bootstrap, BootPlot, Biplot ExportClasses: SelectVar, GroupProj, DiStatis, Bootstrap Package: KinSwingR Exports: buildPWM, cleanAnnotation, scoreSequences, swing, viewPWM Package: kissDE Exports: diffExpressedVariants, kissplice2counts, qualityControl, writeOutputKissDE Package: KnowSeq Exports: batchEffectRemoval, calculateGeneExpressionValues, countsToMatrix, dataPlot, DEGsPathwayVisualization, DEGsToDiseases, downloadPublicSeries, featureSelection, fileMove, gdcClientDownload, geneOntologyEnrichment, getAnnotationFromEnsembl, hisatAlignment, kallistoAlignment, knn_CV, knn_test, limmaDEGsExtraction, plotConfMatrix, rawAlignment, rf_CV, rf_test, RNAseqQA, salmonAlignment, sraToFastq, svm_CV, svm_test, tophatAlignment Package: lapmix Exports: lapmix.Fit, laptopTable, lap.volcanoplot Package: LBE Exports: LBEa, LBEplot, LBE, LBEsummary, LBEwrite Package: ldblock Exports: downloadPopByChr, expandSnpSet, hmld, ldByGene, ldmat, s3_1kg, stack1kg ExportMethods: ldmat Package: LEA Exports: read.geno, write.geno, read.lfmm, write.lfmm, read.env, write.env, read.zscore, geno2lfmm, lfmm2geno, ped2geno, ped2lfmm, vcf2geno, vcf2lfmm, ancestrymap2lfmm, ancestrymap2geno, struct2geno, create.dataset, snmf, cross.entropy.estimation, pca, lfmm ExportMethods: show, summary, load.snmfProject, remove.snmfProject, import.snmfProject, export.snmfProject, combine.snmfProject, load.lfmmProject, remove.lfmmProject, import.lfmmProject, export.lfmmProject, combine.lfmmProject, load.pcaProject, remove.pcaProject, import.pcaProject, export.pcaProject, Q, G, plot, z.scores, lfmm.pvalues, snmf.pvalues, cross.entropy, tracy.widom, impute, barchart Package: LedPred Exports: mapFeaturesToCRMs, mcTune, rankFeatures, tuneFeatureNb, createModel, evaluateModelPerformance, scoreData, LedPred Package: les Exports: triangWeight, rectangWeight, gaussWeight, epWeight ExportMethods: plot, show, summary, threshold, regions, ci, export, estimate, chi2, Les ExportClasses: Les Package: levi Exports: LEVIui, levi, readExpColumn Package: lfa Exports: af, af_snp, center, centerscale, lfa, model.gof, pca_af, read.bed, read.tped.recode, sHWE Package: limma ExportMethods: show ExportClasses: RGList, MAList, EListRaw, EList, MArrayLM, TestResults, LargeDataObject, Roast, MDS Package: LINC Exports: linc, justlinc, clusterlinc, singlelinc, getbio, getlinc, plotlinc, querycluster, feature, linctable, getcoexpr, changeOrgDb, results, correlation, assignment, express, history, linCenvir ExportClasses: LINCfeature, LINCsingle, LINCbio, LINCcluster, LINCmatrix Package: LineagePulse Exports: boolFixedPopulation<-, dfAnnotationProc<-, dfResults<-, lsDispModelConst<-, lsDispModelH0<-, lsDispModelH0_NB<-, lsDispModelH1<-, lsDispModelH1_NB<-, lsDropModel<-, lsFitConvergence<-, lsMuModelConst<-, lsMuModelH0<-, lsMuModelH0_NB<-, lsMuModelH1<-, lsMuModelH1_NB<-, matCountsProc<-, matWeights<-, scaDFSplinesDisp<-, scaDFSplinesMu<-, scaOmega<-, strReport<-, strVersion<-, vecAllGenes<-, vecConfoundersDisp<-, vecConfoundersMu<-, vecH0Pop<-, vecNormConst<-, boolFixedPopulations, dfAnnotationProc, dfResults, getFitsDispersion, getFitsDropout, getFitsMean, getNormData, getPostDrop, lsDispModelConst, lsDispModelH0, lsDispModelH0_NB, lsDispModelH1, lsDispModelH1_NB, lsDropModel, lsFitConvergence, lsMuModelConst, lsMuModelH0, lsMuModelH0_NB, lsMuModelH1, lsMuModelH1_NB, matCountsProc, matWeights, plotCellDensity, plotGene, runLineagePulse, scaDFSplinesDisp, scaDFSplinesMu, scaOmega, simulateContinuousDataSet, sortGeneTrajectories, strReport, strVersion, testDropout, vecAllGenes, vecConfoundersDisp, vecConfoundersMu, vecH0Pop, vecNormConst, writeReport ExportMethods: names, [[, $ Package: LinkHD Exports: DataProcessing, LinkData, OTU2Taxa, Read_Data, VarSelection, dAB ExportMethods: sign_values, correl, compromise_coords, Variables, Var_coordinates, VarTable, Trajectories, RQO, Inertia_comp, Inertia_RV, GlobalPlot, Euclid_Im, CorrelationPlot, Compromise_matrix, CompromisePlot ExportClasses: VarSelection, DistStatis Package: Linnorm Exports: Linnorm, Linnorm.limma, Linnorm.PCA, Linnorm.HVar, Linnorm.Cor, Linnorm.HClust, LinearRegression, Linnorm.Norm, LinearRegressionFP, Linnorm.SGenes, Linnorm.DataImput, Linnorm.tSNE, RnaXSim Package: lionessR Exports: lioness, netFun Package: lipidr Exports: %>%, LipidomicsExperiment, add_sample_annotation, annotate_lipids, as_lipidomics_experiment, de_analysis, de_design, fetch_mw_study, filter_by_cv, gen_lipidsets, is_logged, is_normalized, is_summarized, list_mw_studies, lsea, mva, non_parsed_molecules, normalize_istd, normalize_pqn, plot_chain_distribution, plot_class_enrichment, plot_heatmap, plot_lipidclass, plot_molecules, plot_mva, plot_mva_loadings, plot_results_volcano, plot_samples, plot_trend, read_mwTab, read_mw_datamatrix, read_skyline, remove_non_parsed_molecules, set_logged, set_normalized, set_summarized, significant_lipidsets, significant_molecules, summarize_transitions, top_lipids, update_molecule_names, use_interactive_graphics ExportClasses: LipidomicsExperiment Package: LiquidAssociation ExportMethods: CNM.full, CNM.simple, getsGLA, getsLA, GLA, LA, plotGLA Package: lmdme ExportMethods: summary, show, screeplot, residuals, resid, print, permutation, p.values, p.adjust, modelDecomposition, model, loadingplot, lmdme, leverage, fitted.values, fitted, design, decomposition, componentsType, components, coefficients, coef, biplot, F.p.values ExportClasses: lmdme Package: LMGene Exports: genediff, glog, LMGene, lnorm, lnormeS, neweS, norm, psmeans, plotMeanSD, rowaov, tranest, tranestAffyProbeLevel, transeS, pvadjust Package: LOBSTAHS Exports: doLOBscreen, loadLOBdbase, extractLOBdbasedata, getLOBpeaklist, LOBSet, LOBdbase, generateLOBdbase, exportDBtoCSV ExportMethods: show, LOBisoID_diagnostics, LOBisoID_diagnostics<-, polarity, polarity<-, sampnames, sampnames<-, peakdata, peakdata<-, LOBscreen_settings, LOBscreen_settings<-, LOBscreen_diagnostics, LOBscreen_diagnostics<-, num_compounds, num_compounds<-, num_entries, num_entries<-, frag_ID, frag_ID<-, mz, mz<-, exact_parent_neutral_mass, exact_parent_neutral_mass<-, lipid_class, lipid_class<-, species, species<-, adduct, adduct<-, adduct_rank, adduct_rank<-, FA_total_no_C, FA_total_no_C<-, FA_total_no_DB, FA_total_no_DB<-, degree_oxidation, degree_oxidation<-, parent_elem_formula, parent_elem_formula<-, parent_compound_name, parent_compound_name<- ExportClasses: LOBSet, LOBdbase Package: loci2path Exports: check.geneid, eqtlSet, geneSet, loci2pathResult, tissue ExportMethods: resultTable, query, numGene, getWordcloud, getTissueDegree, getPval, getPathDescription, getMat, getHeatmap, geneSetList, eqtlRange, eqtlId, eqtlGene, description, coveredGene ExportClasses: loci2pathResult, geneSet, eqtlSet Package: logicFS Exports: getMatEval, logic.bagging, logic.oob, logic.pimp, logicFS, make.snp.dummy, vim.chisq, vim.ebam, vim.logicFS, vim.norm, vim.signperm, vim.individual, vim.set, contr.none, contr.snps, mlogreg, vim.singleBoth, vim.singleRemove, vim.snp, vim.input, vim.set, vim.approxPval, vim.permInput, vim.permSNP, vim.permSet, getXy, survivalFS Package: logitT Exports: logitTAffy Package: Logolas Exports: GetConsensusSeq, get_logo_heights, get_plot, get_viewport_logo, logo_pssm, logomaker, makemylogo, nlogomaker, plogomaker Package: LOLA Exports: buildRestrictedUniverse, checkUniverseAppropriateness, extractEnrichmentOverlaps, getRegionFile, getRegionSet, listRegionSets, loadRegionDB, mergeRegionDBs, plotTopLOLAEnrichments, readBed, readCollection, readCollectionAnnotation, readCollectionFiles, readRegionGRL, readRegionSetAnnotation, redefineUserSets, runLOLA, setSharedDataDir, splitFileIntoCollection, writeCombinedEnrichment Package: LoomExperiment Exports: LoomExperiment, LoomFile, LoomGraph, LoomGraphs, RangedLoomExperiment, SingleCellLoomExperiment ExportMethods: show, rowGraphs, rbind, import, export, colGraphs, cbind, rowGraphs<-, colGraphs<-, [ ExportClasses: SingleCellLoomExperiment, RangedLoomExperiment, LoomGraphs, LoomGraph, LoomExperiment Package: LowMACA Exports: allPfamAnalysis ExportMethods: alignSequences, bpAll, entropy, getMutations, mapMutations, nullProfile, parallelize, parallelize<-, lmAlignment, lmEntropy, lmMutations, lmParams, lmParams<-, lmPlot, protter, setup, show, lfm, lfmSingleSequence, lmPlotSingleSequence ExportClasses: LowMACA 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: lpsymphony Exports: lpsymphony_solve_LP Package: LRBaseDbi Exports: makeLRBasePackage, LRBaseDb ExportMethods: columns, keytypes, keys, select, dbconn, dbfile, dbschema, dbInfo, species, lrPackageName, lrNomenclature, lrListDatabases, lrVersion ExportClasses: LRBaseDb Package: lumi Exports: IlluminaID2nuID, addControlData2lumi, addNuID2lumi, addNuId2lumi, bgAdjust, detectOutlier, detectionCall, estimateLumiCV, getChipInfo, getControlData, getControlProbe, getControlType, getNuIDMappingInfo, id2seq, inverseVST, is.nuID, lumiB, lumiExpresso, lumiN, lumiQ, lumiR, lumiR.batch, lumiT, nuID2EntrezID, nuID2IlluminaID, nuID2RefSeqID, nuID2probeID, nuID2targetID, plotCDF, plotControlData, plotDensity, plotHousekeepingGene, plotSampleRelation, plotStringencyGene, plotVST, probeID2nuID, produceGEOPlatformFile, produceGEOSampleInfoTemplate, produceGEOSubmissionFile, rsn, seq2id, ssn, targetID2nuID, vst, rankinvariant, addAnnotationInfo, addControlData2methyLumiM, adjColorBias.quantile, adjColorBias.ssn, beta2m, bgAdjustMethylation, boxplotColorBias, colorBiasSummary, estimateBeta, estimateM, estimateIntensity, estimateMethylationBG, importMethyIDAT, lumiMethyB, lumiMethyC, lumiMethyN, lumiMethyR, m2beta, normalizeMethylation.quantile, normalizeMethylation.ssn, plotColorBias2D, plotColorBias1D, produceMethylationGEOSubmissionFile, smoothQuantileNormalization, lumiMethyStatus, gammaFitEM, methylationCall, plotGammaFit, getChrInfo ExportMethods: beadNum, beadNum<-, boxplot, combine, density, detection, detection<-, getHistory, hist, MAplot, pairs, plot, sampleNames<-, exprs, exprs<-, se.exprs, se.exprs<-, show, summary, [, coerce, controlData, controlData<-, asBigMatrix ExportClasses: LumiBatch Package: LymphoSeq Exports: alignSeq, bhattacharyyaCoefficient, bhattacharyyaMatrix, chordDiagramVDJ, clonalRelatedness, clonality, cloneTrack, commonSeqs, commonSeqsBar, commonSeqsPlot, commonSeqsVenn, differentialAbundance, exportFasta, geneFreq, lorenzCurve, mergeFiles, pairwisePlot, phyloTree, productive, productiveSeq, readImmunoSeq, removeSeq, searchPublished, searchSeq, seqMatrix, similarityMatrix, similarityScore, topFreq, topSeqs, topSeqsPlot, uniqueSeqs Package: M3C Exports: M3C, clustersim, featurefilter, pca, tsne, umap Package: M3Drop Exports: corFS, giniFS, irlbaPcaFS, Consensus_FS, BrenneckeGetVariableGenes, PoissonUMIFeatureSelectionDropouts Package: Maaslin2 Exports: Maaslin2 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: MACPET Exports: AnalysisStatistics, ConvertToPE_BAM, ConvertToPSelf, GetShortestPath, GetSignInteractions, MACPETUlt, PeaksToGRanges, PeaksToNarrowPeak, TagsToGInteractions, exportPeaks ExportMethods: summary, exportPeaks, TagsToGInteractions, PeaksToNarrowPeak, PeaksToGRanges, GetSignInteractions, GetShortestPath, ConvertToPSelf ExportClasses: PSelf, PSFit, PIntra, PInter, GenomeMap Package: MACSQuantifyR Exports: barplot_data, combination_index, generate_report, load_MACSQuant, new_class_MQ, on_plate_selection, pipeline, rData, setPath, sorted ExportClasses: MACSQuant Package: MADSEQ Exports: deltaBIC, normalizeCoverage, plotFraction, plotMadSeq, plotMixture, posterior, prepareCoverageGC, prepareHetero, runMadSeq ExportMethods: summary, posterior, plotMixture, plotMadSeq, plotFraction, deltaBIC ExportClasses: MadSeq Package: maftools Exports: OncogenicPathways, PlotOncogenicPathways, annovarToMaf, clinicalEnrichment, coOncoplot, compareSignatures, drugInteractions, estimateSignatures, extractSignatures, forestPlot, geneCloud, genesToBarcodes, genotypeMatrix, gisticBubblePlot, gisticChromPlot, gisticOncoPlot, icgcSimpleMutationToMAF, inferHeterogeneity, lollipopPlot, lollipopPlot2, mafCompare, mafSummary, mafSurvGroup, mafSurvival, math.score, merge_mafs, mutCountMatrix, oncodrive, oncoplot, oncostrip, pancanComparison, pfamDomains, plotApobecDiff, plotCBSsegments, plotClusters, plotCophenetic, plotEnrichmentResults, plotOncodrive, plotSignatures, plotTiTv, plotVaf, plotmafSummary, prepareMutSig, rainfallPlot, read.maf, readGistic, signatureEnrichment, somaticInteractions, subsetMaf, survGroup, tcgaCompare, titv, trinucleotideMatrix, write.GisticSummary, write.mafSummary ExportMethods: getSampleSummary, getGeneSummary, getFields, getCytobandSummary, getClinicalData ExportClasses: MAF, GISTIC Package: MAGeCKFlute Exports: BatchRemove, CellCycleView, CutoffCalling, DensityDiffView, DensityView, EnrichAB, EnrichAnalyzer, EnrichSquare, EnrichedFilter, EnrichedGeneView, EnrichedView, FluteMLE, FluteRRA, HeatmapView, IdentBarView, KeggPathwayView, MAView, MapRatesView, NormalizeBeta, RankView, ReadBeta, ReadGMT, ReadRRA, ReadsgRRA, ScatterView, Selector, SquareView, TransGeneID, ViolinView, VolcanoView, arrangePathview, enrich.GSE, enrich.HGT, enrich.ORT, getOrg, gsGetter, normalize.loess, sgRankView Package: maigesPack Exports: activeMod, activeModScoreHTML, activeNet, activeNetScoreHTML, addGeneGrps, addPaths, bootstrapCor, bootstrapMI, bootstrapT, calcA, calcW, classifyKNN, classifyKNNsc, classifyLDA, classifyLDAsc, classifySVM, classifySVMsc, compCorr, contrastsFitM, createMaigesRaw, createTDMS, deGenes2by2BootT, deGenes2by2Ttest, deGenes2by2Wilcox, deGenesANOVA, designANOVA, getLabels, heatmapsM, hierMde, hierM, kmeansMde, kmeansM, loadData, MI, normLoc, normOLIN, normRepLoess, normScaleLimma, normScaleMarray, plotGenePair, relNet2TGF, relNetworkB, relNetworkM, robustCorr, selSpots, somMde, somM, summarizeReplicates, tableClass, tablesDE ExportMethods: coerce, show, [ ExportClasses: maigesPreRaw, maigesRaw, maiges, maigesANOVA, maigesDE, maigesDEcluster, maigesClass, maigesRelNetM, maigesRelNetB, maigesActMod, maigesActNet Package: MAIT Exports: Biotransformations, classes, classifRatioClasses, classNum, featureID, featureInfo, featureSigID, identifyMetabolites, LSDResults, metaboliteTable, models, model, scores, MAITbuilder, method, pcaScores, plsScores, pcaLoadings, plsLoadings, loadings, getScoresTable, ovClassifRatioData, ovClassifRatioTable, parameters, peakAggregation, peakAnnotation, plotBoxplot, plotHeatmap, pcaModel, plsModel, plotPLS, plotPCA, pvalues, pvaluesCorrection, rawData, resultsPath, sampleProcessing, sigPeaksTable, spectralSigFeatures, Validation, MAITbuilder ExportMethods: summary, model, scores, loadings ExportClasses: MAIT, MAIT.Parameters, MAIT.FeatureData, MAIT.FeatureInfo, MAIT.PhenoData, MAIT.RawData, MAIT.Validation Package: makecdfenv Exports: getInfoInFile, make.cdf.env, make.cdf.package, pmormm, read.cdffile ExportMethods: name.levels<-, name.levels, pbase.levels<-, pbase.levels, pbase<-, pbase, show, tbase.levels<-, tbase.levels, tbase<-, tbase ExportClasses: Cdf Package: MantelCorr Exports: ClusterGeneList, ClusterList, DistMatrices, GetClusters, MantelCorrs, PermutationTest Package: mAPKL ExportClasses: mAPKLRes, DataLD, Classify, Annot, NetAttr Package: maPredictDSC Exports: predictDSC, aggregateDSC, perfDSC Package: mapscape Exports: mapscape, mapscapeOutput, renderMapscape Package: marray Exports: controlCode, mapGeneInfo, widget.mapGeneInfo, htmlPage, opVersionID, table2html, rbind.marrayInfo, cbind.marrayRaw, cbind.marrayNorm, maNum2Logic, maGeneTable, maCompPlate, maInd2Coord, maCoord2Ind, maCompCoord, maCompInd, maCompLayout, maGenControls, maDotsMatch, maPlate<-, maControls<-, read.marrayLayout, read.marrayInfo, read.marrayRaw, read.Spot, read.GenePix, read.Agilent, read.Galfile, read.SMD, checkTargetInfo, maNormMain, maNorm, maNormScale, maMed, maNormMed, maLoess, maNormLoess, ma2D, maNorm2D, maMAD, maNormMAD, maCompNormEq, maCompNormA, write.marray, write.xls, write.list, plot.marrayRaw, plot.marrayNorm, maDotsDefaults, maDefaultPar, maBoxplot, maPlot.func, maText, maLowessLines, maLoessLines, maLegendLines, maPlot, maImage.func, maImage, maPalette, maColorBar, maTop, maSelectGnames, stat.confband.text, stat.gnames, findID, mean.na, var.na, cor.na, length.na, log.na, quantile.na, order.na, scale.na, prod.na, rm.na, widget.marrayLayout, widget.marrayInfo, widget.marrayRaw, widget.TwoSamples, maTwoSamples, sum.na, URLstring, maInfo, addLines, addText, addPoints, URLstring, read.fname ExportMethods: maLabels, maLabels<-, maInfo<-, maInfo, maNgc<-, maNsr<-, maNsc<-, maNspots<-, maPlate<-, maControls<-, maLayout<-, maGnames<-, maTargets<-, maW<-, maGf<-, maRf<-, maGb<-, maRb<-, maA<-, maM<-, maMloc<-, maMscale<-, maNotes<-, coerce, maNspots, maNgr<-, maNgc, maNsr, maNsc, maSub, maPlate, maNotes, maGridRow, maGridCol, maSpotRow, maSpotCol, maPrintTip, maRf, maGf, maRb, maGb, maW, maLR, maLG, maM, maA, maLayout, maNgr, maControls, maNsamples, maGnames, maTargets, maMloc, maMscale, maNormCall, boxplot, image, points, text, lines, summary, show, [ ExportClasses: marrayInfo, marrayLayout, marrayRaw, marrayNorm, ShowLargeObject Package: martini Exports: get_GI_network, get_GM_network, get_GS_network, ldweight_edges, scones, scones.cv, search_cones, simulate_causal_snps, simulate_phenotype Package: maser Exports: PSI, availableFeaturesUniprotKB, boxplot_PSI_levels, display, dotplot, filterByCoverage, filterByEventId, geneEvents, mapProteinFeaturesToEvents, mapTranscriptsToEvents, maser, pca, plotGenePSI, plotTranscripts, plotUniprotKBFeatures, splicingDistribution, topEvents, volcano ExportMethods: summary, counts, annotation, PSI Package: maSigPro Exports: average.rows, get.siggenes, i.rank, make.design.matrix, maSigPro, maSigProUsersGuide, p.vector, PlotGroups, PlotProfiles, position, reg.coeffs, see.genes, stepback, stepfor, suma2Venn, T.fit, two.ways.stepback, two.ways.stepfor, IsoModel, getDS, seeDS, tableDS, PodiumChange, IsoPlot, getDSPatterns 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: MAST Exports: cData<-, CoefficientHypothesis, FluidigmAssay, FromFlatDF, FromMatrix, Hypothesis, LRT, SceToSingleCellAssay, assay_idx, bootVcov1, burdenOfFiltering, cData, calcZ, collectResiduals, combined_residuals_hook, computeEtFromCt, condSd, condmean, continuous_residuals_hook, convertMASTClassicToSingleCellAssay, defaultPrior, deviance_residuals_hook, discrete_residuals_hook, expavg, filterLowExpressedGenes, fitted_phat, freq, getConcordance, getLogFC, getrc, getss, getwellKey, getwss, gseaAfterBoot, gsea_control, hushWarning, impute, invlogit, logFC, logmean, lrTest, mast_filter, melt.SingleCellAssay, numexp, partialScore, plotSCAConcordance, primerAverage, read.fluidigm, stat_ell, thresholdSCRNACountMatrix, waldTest, zlm, zlm.SingleCellAssay ExportMethods: vcov, update, summary, subset, split, show, se.coef, logLik, combine, cData, LRT, colData<-, cData<- Package: matchBox Exports: calcHypPI, computeCat, plotCat, filterRedundant, mergeData Package: MatrixRider ExportMethods: getSeqOccupancy Package: matter Exports: drle, is.drle, matter, matter_vec, matter_mat, matter_arr, matter_list, matter_str, matter_fc, matter_df, rep_vt, sparse_mat, is.matter, as.matter, is.sparse, as.sparse, is.virtual, as.virtual, virtual_mat, virtual_df, struct, s_range, s_min, s_max, s_prod, s_sum, s_mean, s_var, s_sd, s_any, s_all, stat_c, colstreamStats, rowstreamStats, chunk_apply, chunk_mapply, atoms, uuid, hex2raw, raw2hex, make_filemode, common_filemode, sizeof, make_datamode, convert_datamode, widest_datamode, vm_used, binvec, locmax, bsearch, mem, profmem ExportMethods: prcomp, biglm, bigglm, scale, apply, lapply, sapply, colStats, rowStats, head, tail, range, min, max, prod, sum, mean, var, sd, any, all, colSums, colMeans, colVars, colSds, rowSums, rowMeans, rowVars, rowSds, which, Arith, Compare, Logic, exp, log, log2, log10, %*%, [, [<-, $, $<-, c, combine, cbind, rbind, lengths, length, length<-, dim, dim<-, names, names<-, dimnames, dimnames<-, levels, levels<-, t, crossprod, tcrossprod, keys, keys<-, tolerance, tolerance<-, combiner, combiner<-, describe_for_display, preview_for_display, checksum, adata, atomdata, atomdata<-, datamode, datamode<-, paths, paths<-, path, path<-, filemode, filemode<-, readonly, readonly<-, chunksize, chunksize<-, as.altrep, as.vector, as.matrix, as.array, as.list, as.factor, as.data.frame ExportClasses: drle, matter, matter_vec, matter_mat, matter_matc, matter_matr, matter_arr, matter_list, matter_str, matter_fc, matter_df, rep_vt, sparse_mat, sparse_matc, sparse_matr, virtual_mat, virtual_matc, virtual_matr, virtual_tbl, virtual_df Package: MaxContrastProjection Exports: calcContrast, contrastProjection, fixGaussianBlur, getContrastStack, getIndexMap, intensityProjection, projection_fromMap, validateVariables Package: MBASED Exports: runMBASED Package: MBCB Exports: mbcb.parseFile, mbcb.correct, mbcb.main, bg.rma, bg.mcmc, mbcb.gui Package: mbkmeans Exports: blocksize, compute_wcss, mini_batch, predict_mini_batch ExportMethods: mbkmeans Package: mcaGUI Exports: mcaGUI, pmg.gw, pmg.add, pmg.addMenubar, pmg.eval, pmgRepeatTrials, plotecdf, kurtosis, cluster, richness, diversityfun, principle_component, bootstrap, skewness Package: MCbiclust Exports: CVEval, CVPlot, CorScoreCalc, FindSeed, ForkClassifier, GOEnrichmentAnalysis, HclustGenesHiCor, MultiSampleSortPrep, PC1Align, PC1VecFun, PointScoreCalc, SampleSort, SilhouetteClustGroups, ThresholdBic Package: mCSEA Exports: mCSEAPlot, mCSEAPlotGSEA, mCSEATest, rankProbes, mCSEAIntegrate Package: mdgsa Exports: annotFilter, annotList2mat, annotMat2list, getGOnames, getKEGGnames, getOntology, goLeaves, indexTransform, mdGsa, mdPat, plotMdGsa, propagateGO, pval2index, revList, splitOntologies, transferIndex, uvGsa, uvPat, uvSignif Package: mdp Exports: compute_zscore, mdp, sample_plot Package: mdqc Exports: mdqc, prcomp.robust Package: MDTS Exports: calcBins, calcCounts, calcMD, denovoDeletions, getMetaData, normalizeCounts, segmentMD, visualizeDeletion Package: MeasurementError.cor Exports: cor.me.vector, cor.me.matrix Package: MEB Exports: MEB Package: MEDIPS ExportMethods: sample_name, genome_name, number_regions, chr_names, chr_lengths, genome_count, extend, show, window_size, shifted, uniq ExportClasses: MEDIPSset, COUPLINGset Package: MEDME ExportMethods: initialize, chr, pos, logR, smoothed, AMS, RMS, CG, org, [, show ExportClasses: MEDMEset Package: MEIGOR Exports: CeSSR, CeVNSR, essR_multistart, MEIGO, rvnds_hamming, essR, runBayesFit, cur_params Package: Melissa Exports: binarise_files, create_melissa_data_obj, eval_cluster_performance, eval_imputation_performance, filter_by_coverage_across_cells, filter_by_cpg_coverage, filter_by_variability, impute_met_state, melissa, melissa_gibbs, partition_dataset, plot_melissa_profiles Package: MergeMaid Exports: mergeExprs ExportMethods: exprs, geneNames, names, notes, phenoData, length, show, summary, geneStudy, coeff, stdcoeff, zscore, pairwise.cors, maxcors, integrative.cors, modelOutcome, intCor, plot, hist, intcorDens, intersection, exprs<-, geneNames<-, names<-, notes<-, phenoData<-, geneStudy<-, coeff<-, stdcoeff<-, zscore<- ExportClasses: mergeExpressionSet, mergeCor, mergeCoeff Package: MeSHDbi Exports: makeGeneMeSHPackage, MeSHDb ExportMethods: columns, keytypes, keys, select, dbconn, dbfile, dbschema, dbInfo, species, packageName, nomenclature, listDatabases, meshVersion ExportClasses: MeSHDb Package: meshes Exports: cnetplot, dotplot, emapplot, enrichMeSH, geneID, geneInCategory, geneSim, gseMeSH, gseaplot, heatplot, meshSim, meshdata, ridgeplot Package: meshr ExportMethods: meshHyperGTest, meshIds, meshCategory, meshAnnotation, meshDatabase, show, summary, save.pdf, initialize, geneIds, universeGeneIds, universeGeneIds<-, annotation, annotation<-, category, category<-, database, database<-, pvalueCutoff, pvalueCutoff<-, pAdjust, pAdjust<-, makeValidParams ExportClasses: MeSHHyperGParams, MeSHHyperGResult Package: messina Exports: messina, messinaDE, messinaSurv, messinaTopResults ExportMethods: show, plot ExportClasses: MessinaSurvResult, MessinaClassResult Package: metaArray Exports: poe.mcmc, poe.em, intcor Package: Metab Exports: MetReport, normalizeByInternalStandard, normalizeByBiomass, removeFalsePositives, buildLib, htest, MetReportNames Package: metabomxtr ExportMethods: xdesign, zdesign, yvals Package: MetaboSignal Exports: MS_keggNetwork, MS_reactionNetwork, MS_distances, MS_shortestPathsNetwork, MS_changeNames, MS_shortestPaths, MS_topologyFilter, MS_nodeBW, MS_exportCytoscape, MS_keggFinder, MS_convertGene, MS_findMappedNodes, MS_replaceNode, MS_removeDrugs, MS_removeNode, MS_tissueFilter, MS2_ppiNetwork, MS2_mergeNetworks, MS_getPathIds Package: metaCCA Exports: estimateSyy, metaCcaGp, metaCcaPlusGp Package: MetaCyto Exports: autoCluster.batch, clusterStats, collectData, densityPlot, fcsInfoParser, filterLabels, findCutoff, flowHC, flowSOM.MC, glmAnalysis, labelCluster, labelSummary, markerFinder, metaAnalysis, nameUpdator, panelSummary, plotGA, preprocessing, preprocessing.batch, sampleInfoParser, searchCluster, searchCluster.batch, set2Frame Package: metagene Exports: metagene, get_demo_bam_files, get_demo_regions, get_demo_metagene, get_demo_design, permutation_test, plot_metagene Package: metagene2 Exports: Bam_Handler, get_demo_bam_files, get_demo_design, get_demo_metagene, get_demo_region_filenames, get_demo_regions, get_demo_rna_bam_files, get_demo_rna_regions, metagene2, plot_metagene Package: metagenomeFeatures Exports: %>%, get_gg13.8_85MgDb, mgDb_meta, mgDb_seq, mgDb_taxa, mgDb_tree, mgF_meta, mgF_seq, mgF_taxa, mgF_tree, mgFeatures, newMgDb, taxa_columns, taxa_keys ExportMethods: taxa_keytypes, show, mgDb_select, annotateFeatures ExportClasses: mgFeatures, MgDb Package: metagenomeSeq Exports: aggregateByTaxonomy, aggTax, aggregateBySample, aggSamp, biom2MRexperiment, calculateEffectiveSamples, calcNormFactors, correlationTest, correctIndices, cumNorm, cumNormMat, cumNormStat, cumNormStatFast, expSummary, exportMat, exportStats, fitDO, fitMeta, fitFeatureModel, fitLogNormal, fitPA, fitMultipleTimeSeries, fitSSTimeSeries, fitTimeSeries, fitZig, filterData, load_biom, load_meta, load_metaQ, load_phenoData, loadBiom, loadMeta, loadMetaQ, loadPhenoData, makeLabels, mergeMRexperiments, MRcoefs, MRcounts, MRfulltable, MRtable, MRexperiment2biom, plotBubble, plotCorr, plotGenus, plotMRheatmap, plotOTU, plotOrd, plotRare, plotFeature, plotTimeSeries, plotClassTimeSeries, uniqueFeatures, returnAppropriateObj, ssFit, ssIntervalCandidate, ssPerm, ssPermAnalysis, ts2MRexperiment, trapz, zigControl, newMRexperiment, posteriorProbs, wrenchNorm ExportMethods: [, colSums, rowSums, colMeans, rowMeans, normFactors, normFactors<-, libSize, libSize<-, MRihw ExportClasses: MRexperiment, fitFeatureModelResults, fitZigResults Package: metahdep Exports: metahdep.FEMA, metahdep.format, metahdep.HBLM, metahdep, metahdep.REMA, getPLM.es, metahdep.list2dataframe, LinMod.MetAn.dep.REMA, LinMod.REMA.dep, LinMod.REMA.delta.split, LinMod.HBLM.fast.dep, new.LinMod.HBLM.fast.dep.delta.split, LinMod.MetAn.dep.FEMA, metahdep.check.X, get.M, tr, id, center.columns, mod, get.varsigma.v Package: metaMS Exports: runGC, runLC, peakDetection, matchExpSpec, write.msp, construct.msp, filter.msp, read.msp, to.msp, addRI, treat.DB, matchSamples2DB, matchSamples2Samples, constructExpPseudoSpectra, getFeatureInfo, getAnnotationMat, AnnotateFeature, AnnotateTable, plotPseudoSpectrum, processStandards, alignmentLC, runCAMERA, getAnnotationLC, getPeakTable, createSTDdbGC, createSTDdbLC, readStdInfo, generateStdDBGC, generateStdDBLC, metaMSsettings, metaSetting ExportMethods: metaSetting, metaSetting<-, show ExportClasses: metaMSsettings Package: MetaNeighbor Exports: MetaNeighbor, MetaNeighborUS, neighborVoting, topHits, variableGenes Package: metaSeq Exports: meta.readData, meta.oneside.noiseq, Fisher.test, Stouffer.test, other.oneside.pvalues, Accelerate.NOISeq, Reset.Accelerate.NOISeq Package: metaseqR Exports: as.class.vector, calc.otr, calc.f1score, check.contrast.format, check.file.args, check.libsize, check.num.args, check.packages, check.parallel, check.text.args, combine.bonferroni, combine.maxp, combine.minp, combine.simes, combine.weight, construct.gene.model, diagplot.avg.ftd, diagplot.boxplot, diagplot.cor, diagplot.de.heatmap, diagplot.edaseq, diagplot.filtered, diagplot.ftd, diagplot.mds, diagplot.metaseqr, diagplot.noiseq, diagplot.pairs, diagplot.roc, diagplot.venn, diagplot.volcano, disp, downsample.counts, estimate.aufc.weights, estimate.sim.params, filter.exons, filter.genes, filter.high, filter.low, get.annotation, get.biotypes, get.dataset, get.defaults, get.ensembl.annotation, get.exon.attributes, get.gc.content, get.gene.attributes, get.host, get.preset.opts, get.transcript.utr.attributes, get.ucsc.annotation, get.ucsc.credentials, get.ucsc.dbl, get.ucsc.tabledef, get.ucsc.query, get.valid.chrs, get.weights, load.bs.genome, make.contrast.list, make.fold.change, make.grid, make.html.body, make.html.cells, make.html.header, make.html.rows, make.html.table, make.matrix, make.permutation, make.sample.list, make.sim.data.tcc, make.sim.data.sd, make.stat, make.transformation, make.venn.areas, make.venn.colorscheme, make.venn.counts, make.venn.pairs, metaseqr, normalize.deseq, normalize.edaseq, normalize.edger, normalize.nbpseq, normalize.noiseq, fisher.method, fisher.method.perm, fisher.sum, read2count, read.targets, reduce.exons, reduce.gene.data, stat.bayseq, stat.deseq, stat.edger, stat.limma, stat.nbpseq, stat.noiseq, validate.alg.args, validate.list.args, wapply Package: metavizr Exports: generateSelection, metavizControl, replaceNAFeatures, setMetavizStandalone, startMetaviz, startMetavizStandalone, validateObject ExportClasses: MetavizApp, EpivizMetagenomicsDataTimeSeries, EpivizMetagenomicsDataInnerNodes, EpivizMetagenomicsData Package: MetaVolcanoR Exports: calc_vi, collapse_deg, combining_mv, cum_freq_data, deg_def, draw_cum_freq, draw_degbar, draw_forest, plot_mv, plot_rem, rem_mv, remodel, rename_col, set_degbar_data, votecount_mv Package: MetCirc Exports: cart2Polar, circosLegend, compare_Spectra, convertMsp2Spectra, createLink0df, createLinkDf, cutLinkDf, getLinkDfIndices, highlight, minFragCart2Polar, neutralloss, normalizeddotproduct, orderSimilarityMatrix, plotCircos, plotSpectra, shinyCircos, thresholdLinkDf Package: MethCP Exports: MethCP, MethCPFromStat, calcLociStat, calcLociStatTimeCourse, createBsseqObject, getSigRegion, segmentMethCP ExportMethods: show ExportClasses: MethCP Package: methimpute Exports: binCounts, binMethylome, binPositions, binomialTestMethylation, callMethylation, callMethylationSeparate, collapseBins, distanceCorrelation, estimateTransDist, exportMethylome, extractCytosinesFromFASTA, getDistinctColors, getStateColors, importBSMAP, importBSSeeker, importBismark, importMethylpy, inflateMethylome, loadFromFiles, plotConvergence, plotEnrichment, plotHistogram, plotPosteriorDistance, plotScatter, plotTransitionProbs Package: methInheritSim Exports: runSim Package: MethPed Exports: MethPed, checkNA, probeMis Package: methrix Exports: combine_methrix, convert_HDF5_methrix, convert_methrix, coverage_filter, extract_CPGs, get_matrix, get_region_summary, get_stats, load_HDF5_methrix, mask_methrix, methrix2bsseq, methrix_pca, methrix_report, order_by_sd, plot_coverage, plot_density, plot_pca, plot_stats, plot_violin, read_bedgraphs, region_filter, remove_snps, remove_uncovered, save_HDF5_methrix, subset_methrix, write_bedgraphs ExportClasses: methrix Package: methVisual Exports: plotAbsMethyl, MethLollipops, heatMapMeth, matrixSNP, plotMatrixSNP, methCA, methFisherTest, methWhitneyUTest, cgInAlign, findNonAligned, Cooccurrence, MethAlignNW, cgMethFinder, makeDataMethGFF, MethDataInput, selectRefSeq, readBisulfFASTA, makeLocalExpDir, makeTabFilePath, MethylQC, coversionGenom Package: methyAnalysis Exports: MethyGenoSet, annotateDMRInfo, annotateGRanges, detectDMR.slideWin, export.methyGenoSet, getContinuousRegion, identifySigDMR, export.DMRInfo, MethyLumiM2GenoSet, smoothMethyData, createTranscriptTrack, buildAnnotationTracks, heatmapByChromosome, plotHeatmapByGene, plotMethylationHeatmapByGene, plotTracksWithDataTrackInfo, checkChrName, estimateCMR.methylation, estimateMethySeq, filterBisulfiteVariant, getCoverage, identifyCpG, updateMethyGenoSet, rowRanges, colData, assays ExportMethods: asBigMatrix, exprs, exprs<-, methylated, unmethylated, detection, methylated<-, unmethylated<-, detection<-, getHistory, combine, [, coerce, chrNames ExportClasses: MethyGenoSet Package: MethylAid Exports: summarize, visualize ExportMethods: show, combine ExportClasses: summarizedData Package: methylCC Exports: estimatecc ExportMethods: cell_counts ExportClasses: estimatecc Package: methylGSA Exports: barplot, getDescription, getGS, methylRRA, methylglm, methylgometh, prepareAnnot, runExample Package: methylInheritance Exports: calculateSignificantLevel, extractInfo, loadAllRDSResults, loadConvergenceData, mergePermutationAndObservation, plotConvergenceGraph, plotGraph, runObservation, runPermutation Package: methylKit Exports: getSampleID<-, getTreatment<-, PCASamples, adjust.methylC, adjustMethylC, annotate.WithFeature, annotate.WithFeature.Flank, annotate.WithGenicParts, assocComp, bedgraph, calculateDiffMeth, calculateDiffMethDSS, clusterSamples, dataSim, diffMethPerChr, filterByCoverage, get.methylDiff, getAssembly, getContext, getCorrelation, getCoverageStats, getDBPath, getData, getFeatsWithTargetsStats, getFlanks, getMembers, getMethylDiff, getMethylationStats, getSampleID, getTargetAnnotationStats, getTreatment, joinSegmentNeighbours, makeMethylDB, methRead, methSeg, methSeg2bed, normalizeCoverage, percMethylation, plotTargetAnnotation, pool, processBismarkAln, read, read.bed, read.bismark, read.feature.flank, read.transcript.features, reconstruct, regionCounts, removeComp, reorganize, select, selectByOverlap, tileMethylCounts, unite ExportClasses: methylRawListDB, methylRawList, methylRawDB, methylRaw, methylDiffDB, methylDiff, methylBaseDB, methylBase Package: MethylMix Exports: ClusterProbes, Download_DNAmethylation, Download_GeneExpression, GetData, MethylMix, MethylMix_ModelGeneExpression, MethylMix_PlotModel, MethylMix_Predict, Preprocess_DNAmethylation, Preprocess_GeneExpression Package: methylPipe ExportMethods: [[, [[<-, [, $, show, chr, binC, binmC, binrC, nbins, binscore, binscore<-, mCsmoothing, findDMR, methstats ExportClasses: GEcollection, GElist, BSdata, BSdataSet Package: MethylSeekR Exports: readMethylome, readSNPTable, removeSNPs, plotAlphaDistributionOneChr, segmentPMDs, plotPMDSegmentation, savePMDSegments, calculateFDRs, segmentUMRsLMRs, plotFinalSegmentation, saveUMRLMRSegments Package: methylumi Exports: methylumiR, extractBarcodeAndPosition, normalizeMethyLumiSet, getAssayDataNameSubstitutions, estimateM, methylumIDAT, lumIDAT, methylumiCSV, lumiCSV, methylumi.diagnostics, qc.probe.plot, cy3, cy5, getBarcodes, stripBeadNs, stripBeadSDs, stripMethyLumiSet, psummary, negctls.stderr, methylumi.bgcorr, IDATtoMatrix, IDATsToMatrices, designItoMandU, designIItoMandU, mergeProbeDesigns, NChannelSetToMethyLumiSet, stripOOB, plotNegOob, tcgaPipeline, .mclapply ExportMethods: getHistory, betas, pvals, exprs, summary, show, combine, hist, pairs, [, QCdata, plotSampleIntensities, qcplot, total.intensity, methylated, unmethylated, unmethylated<-, methylated<-, QCdata<-, exprs<-, diagnostics, Cy3.N, Cy5.N, pvals<-, betas<-, controlTypes, corplot, negctls.stderr, controlData, controlData<-, detection, detection<-, unmethylated.N, unmethylated.N<-, pval.detect<-, pval.detect, sampleNAs, probeNAs, plotNAs, normctls, negctls, methylated.N, methylated.N<-, featureFilter, varFilter, intensities.OOB, intensities.IB, negnorm, Cy3<-, Cy5<-, intensities.OOB.allelic, intensitiesByChannel, intensities.M, intensities.U, combine27k450k, dataType, dataType<- ExportClasses: MethyLumiSet, MethyLumiQC, MethyLumi, MethyLumiM, methylData Package: methyvim Exports: .methytmle, fdr_msa, methyheat, methyvim, methyvolc, vim ExportClasses: methytmle Package: MetID Exports: get_scores_for_LC_MS Package: MetNet Exports: aracne, bayes, clr, combineStructuralStatistical, consensusAdjacency, correlation, createStatisticalAdjacency, createStatisticalAdjacencyList, createStructuralAdjacency, lasso, randomForest, rtCorrection Package: mfa Exports: calculate_chi, create_synthetic, empirical_lambda, mfa, plot_chi, plot_dropout_relationship, plot_mfa_autocorr, plot_mfa_trace Package: Mfuzz Exports: acore, cselection, Dmin, fill.NA, filter.NA, filter.std, filter.std, kmeans2, kmeans2.plot, mestimate, membership, mfuzz, mfuzz.plot, mfuzz.plot2, Mfuzzgui, mfuzzColorBar, overlap, overlap.plot, partcoef, randomise, standardise, standardise2, top.count, table2eset Package: MGFM Exports: getMarkerGenes, getHtmlpage Package: MGFR Exports: getMarkerGenes.rnaseq, getMarkerGenes.rnaseq.html Package: mgsa Exports: readGAF ExportMethods: subMgsaSets, studySetSizeInPopulation, steps, show, setsResults, setsMcmcPost, setAnnotations, restarts, populationSize, plot, pPost, pMcmcPost, nsamples, mgsa, length, itemIndices, itemAnnotations, betaPost, betaMcmcPost, alphaPost, alphaMcmcPost ExportClasses: MgsaSets, MgsaResults, MgsaMcmcResults, MgsaGoSets Package: MiChip Exports: parseRawData, outputAnnotatedDataMatrix, returnAnnotatedDataMatrix, removeUnwantedRows, standardRemoveRows, myForgivingMedian, setIntensityCutoff, correctForFlags, summarizeIntensitiesAsMedian, normalizePerChipMedian, boxplotData, boxplotDataNoFile, plotIntensitiesScatter, workedExampleMedianNormalize, workedExampleNotNormalizedData Package: microbiome Exports: abundances, aggregate_taxa, aggregate_top_taxa, alpha, associate, baseline, bfratio, bimodality, boxplot_abundance, collapse_replicates, core, core_abundance, core_members, coverage, default_colors, divergence, diversities, diversity, dominance, dominant, evenness, gktau, global, group_age, group_bmi, heat, hotplot, inequality, intermediate_stability, is_compositional, log_modulo_skewness, low_abundance, map_levels, merge_taxa2, meta, neat, neatsort, noncore_members, plot_atlas, plot_composition, plot_core, plot_density, plot_frequencies, plot_landscape, plot_regression, plot_taxa_prevalence, plot_tipping, potential_analysis, prevalence, quiet, rare, rare_abundance, rare_members, rarity, read_biom2phyloseq, read_csv2phyloseq, read_mothur2phyloseq, read_phyloseq, readcount, remove_samples, remove_taxa, richness, spreadplot, summarize_phyloseq, taxa, time_normalize, time_sort, timesplit, top, top_taxa, transform, write_phyloseq Package: microbiomeDASim Exports: gen_norm_microbiome, ggplot_spaghetti, mean_trend, mvrnorm_corr_gen, mvrnorm_sim Package: microRNA Exports: get_selfhyb_subseq, show_selfhyb_counts, show_selfhyb_lengths, seedRegions, matchSeeds, RNA2DNA Package: mimager Exports: arank, arle, marray, mimage ExportMethods: mimage, marray Package: MIMOSA Exports: ConstructMIMOSAExpressionSet, MIMOSA, MIMOSAExpressionSet, asinh_trans, boxplotMIMOSAResultList, combine.MIMOSA, countsTable, fdr, getW, getZ, volcanoPlot Package: MineICA Exports: annot2Color, annotFeatures, annotFeaturesComp, annotFeaturesWithBiomaRt, annotInGene, annotReciprocal, buildIcaSet, buildMineICAParams, clusterFastICARuns, clusterSamplesByComp, clusterSamplesByComp_multiple, clusVarAnalysis, compareAn, compareAn2graphfile, compareGenes, cor2An, getProj, getSdExpr, hypergeoAn, nbOccInComp, nodeAttrs, plotAllMix, plotCorGraph, plot_heatmapsOnSel, plotMix, plotPosAnnotInComp, plotPosSamplesInComp, qualVarAnalysis, quantVarAnalysis, relativePath, runAn, runCompareIcaSets, runEnrich, runICA, selectContrib, selectFeatures_IQR, selectWitnessGenes, writeGenes, writeHtmlResTestsByAnnot, writeProjByComp, writeRnkFiles ExportMethods: dat, dat<-, datByGene, datByGene<-, nbComp, organism, organism<-, A, Alist, A<-, S, S<-, SByGene, SByGene<-, [, [<-, getComp, indComp, indComp<-, compNames, compNames<-, witGenes<-, witGenes, Slist, SlistByGene, chipVersion, chipVersion<-, chipManu<-, chipManu, refSamples<-, refSamples, typeID<-, typeID, annotfile, annotfile<-, Afile, Afile<-, Sfile, Sfile<-, datfile, datfile<-, resPath, resPath<-, genesPath, genesPath<-, annot2col, annot2col<-, selCutoff, selCutoff<-, pvalCutoff, pvalCutoff<-, geneNames, mart, mart<- ExportClasses: IcaSet, MineICAParams Package: minet Exports: aracne, build.mim, clr, fscores, minet, mrnet, mrnetb, pr, rates, show.pr, show.roc, auc.pr, auc.roc, validate Package: minfi Exports: getManifest, getProbeInfo, getManifestInfo, IlluminaMethylationManifest, IlluminaMethylationAnnotation, getControlAddress, getRed, getGreen, getNBeads, getMeth, getUnmeth, getBeta, getM, getCN, getMethSignal, getOOB, getSnpBeta, dropMethylationLoci, getLocations, getAnnotation, getAnnotationObject, mapToGenome, subsetByLoci, getIslandStatus, getProbeType, getSnpInfo, addSnpInfo, dropLociWithSnps, normalize.illumina.control, bgcorrect.illumina, preprocessRaw, preprocessIllumina, preprocessSWAN, preprocessQuantile, preprocessFunnorm, preprocessNoob, RGChannelSet, RGChannelSetExtended, MethylSet, RatioSet, GenomicMethylSet, GenomicRatioSet, read.450k, read.450k.sheet, read.450k.exp, read.metharray, read.metharray.sheet, read.metharray.exp, getGenomicRatioSetFromGEO, makeGenomicRatioSetFromMatrix, readGEORawFile, readTCGA, logit2, ilogit2, dmpFinder, mdsPlot, plotCpg, plotBetasByType, detectionP, qcReport, controlStripPlot, densityBeanPlot, densityPlot, getQC, plotQC, addQC, minfiQC, fixMethOutliers, getSex, plotSex, addSex, bumphunter, blockFinder, cpgCollapse, estimateCellCounts, gaphunter, compartments, createCorMatrix, extractAB, convertArray, combineArrays ExportMethods: show, initialize, getBeta, getM, getCN, getMeth, getUnmeth, getManifest, annotation, annotation<-, preprocessMethod, combine, mapToGenome, ratioConvert, bumphunter, pData, pData<-, sampleNames, sampleNames<-, featureNames, featureNames<-, coerce ExportClasses: RGChannelSet, RGChannelSetExtended, MethylSet, RatioSet, GenomicMethylSet, GenomicRatioSet, IlluminaMethylationManifest, IlluminaMethylationAnnotation 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: MIRA Exports: BSBinAggregate, BSreadBiSeq, SummarizedExperimentToDataTable, addMethPropCol, aggregateMethyl, binRegion, bsseqToDataTable, calcMIRAScore, plotMIRAProfiles, plotMIRAScores, rbindNamedList Package: MiRaGE Exports: MiRaGE, HS_conv_id, MM_conv_id, id_conv_gen, TBL2_HS_gen, TBL2_MM_gen, getMiRaGEData Package: miRBaseConverter Exports: checkMiRNAAlive, checkMiRNAFamily, checkMiRNAVersion, getAllMiRNAs, getAllSpecies, getAllVersionInfo, getMiRNAHistory, getMiRNASequence, getMiRNATable, goTo_miRBase, goTo_miRNAFamily, miRNAVersionConvert, miRNA_AccessionToName, miRNA_MatureToPrecursor, miRNA_NameToAccession, miRNA_PrecursorToMature Package: miRcomp Exports: accuracy, precision, limitOfDetection, titrationResponse, completeFeatures, qualityAssessment, expressionComp, miRcompShinyApp Package: mirIntegrator Exports: integrate_mir, pathways2pdf, plot_augmented_pathway, plot_change, smallest_pathway Package: miRLAB Exports: Borda, BordaTopk, Dcov, DiffExpAnalysis, Elastic, Extopk, GOBPenrichment, Hoeffding, ICPPam50, IDA, ImputeNormData, KEGGenrichment, Kendall, Lasso, MI, Pearson, ProMISe, RDC, Read, ReadExtResult, Spearman, ValidateAll, Validation, ValidationT, Zscore, bRank, convert, experiment, filterAndCompare, getData, identifymiRTargetsByEnsemble, identifymiRTargetsByICPPam50, readHeader Package: miRNAmeConverter Exports: MiRNANameConverter, assessVersion, checkMiRNAName, currentVersion, getMirnasForMirbaseVersion, nOrganisms, nTotalEntries, saveResults, translateMiRNAName, validOrganisms, validVersions ExportMethods: show Package: miRNApath ExportMethods: show ExportClasses: mirnapath Package: miRNAtap Exports: aggregateRanks, getPredictedTargets, getTargetsFromSource, translate ExportMethods: select, keytypes, keys, columns ExportClasses: MirnaDb Package: miRSM Exports: cor_binary, miRSM, module_CEA, module_Coexpress, module_FA, module_GFA, module_NMF, module_ProNet, module_Validate, module_WGCNA, module_biclust, module_clust, module_igraph, module_miRdistribute, module_miRsponge, module_miRtarget, share_miRs Package: miRspongeR Exports: integrateMethod, moduleDEA, moduleFEA, moduleSurvival, netModule, querymiRTargetbinding, spongeMethod, spongeValidate Package: Mirsynergy Exports: mirsynergy, print_modules2, plot_modules, summary_modules, plot_module_summary, tabular_module Package: missRows Exports: MIDTList, imputedData, MIMFA, missPattern, plotInd, plotVar, tuneM, missingIndv, compromise, configurations, imputedIndv, MIparam ExportClasses: MIDTList Package: mitoODE Exports: plotfit, plotk, getp0, fitmodel, loadFittedData, figure1, figure2, figure3a, figure3b, figure4 Package: mixOmics Exports: auroc, background.predict, block.pls, block.plsda, block.spls, block.splsda, cim, cimDiablo, circosPlot, color.jet, color.GreenRed, color.spectral, color.mixo, explained_variance, get.BER, get.confusion_matrix, image.tune.rcc, imgCor, ipca, logratio.transfo, map, mat.rank, mint.block.pls, mint.block.plsda, mint.block.spls, mint.block.splsda, mint.pca, mint.pls, mint.plsda, mint.spls, mint.splsda, mixOmics, nearZeroVar, network, nipals, pca, perf, plotArrow, plotDiablo, plotIndiv, plotLoadings, plotVar, pls, plsda, rcc, selectVar, sipca, spca, spls, splsda, study_split, tune, tune.mint.splsda, tune.spls, tune.splsda, tune.block.splsda, tune.splslevel, tune.pca, tune.rcc, unmap, vip, withinVariation, wrapper.rgcca, wrapper.sgcca, wrapper.sgccda Package: MLInterfaces Exports: randomForestI, knnI, dldaI, nnetI, rpartI, ldaI, svmI, ldaI.predParms, qdaI, glmI.logistic, RABI, lvqI, naiveBayesI, baggingI, knn2, dlda2, rab, lvq, RAB, DAB, plsda2, svm2, ksvm2, xvalSpec, getVarImp, balKfold.xvspec, rdacvI, rdacvML, rdaI, rdaML, plotXvalRDA, makeLearnerSchema, standardMLIConverter, sldaI, fs.absT, fs.probT, ksvmI, knn.cvI, knn.cv2, adaI, fs.topVariance, hclustI, kmeansI, pamI, blackboostI, gbm2, BgbmI, plsdaI, confuTab, hclustWidget, mlearnWidget, projectLearnerToGrid, plspinHcube ExportMethods: learnerIn3D, plotOne, plot, show, RObject, confuMat, trainInd, precision, recall, sensitivity, macroF1, F1, acc, tp, tn, fp, fn, specificity, MLearn, planarPlot, Predict, getVarImp, trainScores, trainPredictions, testScores, testPredictions, predictions, predScores, predScore, fsHistory, report, getDist, getConverter ExportClasses: projectedLearner, varImpStruct, classifierOutput, learnerSchema, xvalSpec, clusteringOutput Package: MLP Exports: MLP, addGeneSetDescription, getGeneSets, mlpBarplot, plotGOgraph, plotGeneSetSignificance Package: MLSeq Exports: control<-, isModified<-, isUpdated<-, method<-, normalization<-, preProcessing<-, ref<-, availableMethods, classify, confusionMat, control, discreteControl, input, isModified, isUpdated, metaData, method, modelInfo, normalization, preProcessing, predictClassify, printAvailableMethods, ref, selectedGenes, trainParameters, trained, transformation, voomControl ExportMethods: update, transformation, trained, trainParameters, selectedGenes, ref, print, predict, preProcessing, plot, normalization, modelInfo, method, metaData, isUpdated, isModified, input, control, confusionMat, ref<-, preProcessing<-, normalization<-, method<-, isUpdated<-, isModified<-, control<- ExportClasses: voom.train, discrete.train, MLSeqModelInfo, MLSeqMetaData, MLSeq Package: MMAPPR2 Exports: MmapprParam, calculateDistance, generateCandidates, loessFit, mmappr, outputMmapprData, peakRefinement, prePeak, tempOutputFolder ExportMethods: wtFiles, vepFlags, species, refGenome, refFasta, peaks, peakIntervalWidth, param, outputFolder, naCutoff, mutFiles, minMapQuality, minDepth, minBaseQuality, loessOptResolution, loessOptCutFactor, homozygoteCutoff, fileAggregation, distancePower, distance, candidates, wtFiles<-, vepFlags<-, species<-, refGenome<-, refFasta<-, peakIntervalWidth<-, outputFolder<-, naCutoff<-, mutFiles<-, minMapQuality<-, minDepth<-, minBaseQuality<-, loessOptResolution<-, loessOptCutFactor<-, homozygoteCutoff<-, fileAggregation<-, distancePower<- ExportClasses: MmapprParam, MmapprData Package: MMDiff2 Exports: Contrast, Counts, DBAmmd, Dists, Genome, Hists, Reads, Regions, Samples, compDists, compHists, compPvals, estimateFragmentCenters, getPeakReads, metaData, numPeaks, numSamples, plotDISTS4Peak, plotDists, plotPeak, reportResults, runShinyMMDiff2, setContrast, setRegions ExportClasses: DBAmmd Package: MmPalateMiRNA Exports: imputeKNN, fixOutliers, fixMVs, clustPlot ExportMethods: densityplot, levelplot, checkOutliers, checkMVs, filterArray, MADvsMedianPlot, MAplot Package: MMUPHin Exports: adjust_batch, continuous_discover, discrete_discover, lm_meta Package: mnem Exports: bootstrap, clustNEM, createApp, fitacc, fuzzyindex, getAffinity, getIC, hamSim, mnem, mnemh, mnemk, plotConvergence, plotDnf, simData Package: MODA Exports: CompareAllNets, ModuleFrequency, PartitionDensity, PartitionModularity, WeightedModulePartitionAmoutain, WeightedModulePartitionHierarchical, WeightedModulePartitionLouvain, WeightedModulePartitionSpectral, comparemodulestwonets Package: Modstrings Exports: ModDNAString, ModDNAStringSet, ModDNAStringSetList, ModRNAString, ModRNAStringSet, ModRNAStringSetList, QualityScaledModDNAStringSet, QualityScaledModRNAStringSet, combineIntoModstrings, fullName, letterFrequency, modifyNucleotides, nomenclature, readModDNAStringSet, readModRNAStringSet, readQualityScaledModDNAStringSet, readQualityScaledModRNAStringSet, replaceLetterAt, sanitizeFromModomics, sanitizeFromtRNAdb, sanitizeInput, separate, shortName, writeModStringSet, writeQualityScaledModStringSet ExportMethods: show, shortName, seqtype, separate, replaceLetterAt, nomenclature, modifyNucleotides, letterFrequency, hasOnlyBaseLetters, fullName, consensusString, consensusMatrix, combineIntoModstrings, as.vector, as.character, alphabetFrequency, alphabet, XStringSet, XString, Views, seqtype<-, == ExportClasses: QualityScaledModRNAStringSet, QualityScaledModDNAStringSet, ModRNAStringSetList, ModRNAStringSet, ModRNAString, ModDNAStringSetList, ModDNAStringSet, ModDNAString Package: MOFA Exports: DataOptions<-, Dimensions<-, Expectations<-, FeatureIntercepts<-, ImputedData<-, InputData<-, ModelOptions<-, Status<-, TrainData<-, TrainOptions<-, TrainStats<-, factorNames<-, featureNames<-, sampleNames<-, viewNames<-, DataOptions, Dimensions, Expectations, FeatureIntercepts, ImputedData, InputData, ModelOptions, Status, TrainData, TrainOptions, TrainStats, calculateVarianceExplained, clusterSamples, compareFactors, compareModels, createMOFAobject, factorNames, featureNames, getCovariates, getDefaultDataOptions, getDefaultModelOptions, getDefaultTrainOptions, getDimensions, getELBO, getExpectations, getFactors, getImputedData, getTrainData, getWeights, impute, loadModel, makeExampleData, plotDataHeatmap, plotDataOverview, plotDataScatter, plotEnrichment, plotEnrichmentBars, plotEnrichmentDetailed, plotEnrichmentHeatmap, plotFactorBeeswarm, plotFactorCor, plotFactorHist, plotFactorScatter, plotFactorScatters, plotTopWeights, plotVarianceExplained, plotWeights, plotWeightsHeatmap, predict, prepareMOFA, qualityControl, regressCovariates, runEnrichmentAnalysis, runMOFA, sampleNames, selectModel, subsetFactors, subsetSamples, subsetViews, trainCurveELBO, trainCurveFactors, viewNames ExportMethods: viewNames, sampleNames, featureNames, factorNames, TrainStats, TrainOptions, TrainData, Status, ModelOptions, InputData, ImputedData, FeatureIntercepts, Expectations, Dimensions, DataOptions, viewNames<-, sampleNames<-, featureNames<-, factorNames<-, TrainStats<-, TrainOptions<-, TrainData<-, Status<-, ModelOptions<-, InputData<-, ImputedData<-, FeatureIntercepts<-, Expectations<-, Dimensions<-, DataOptions<- ExportClasses: MOFAmodel Package: mogsa Exports: decompose.gs.ind, decompose.gs.group, moa, box.gs.feature, mogsa, pairwise.rv, prepGraphite, prepMsigDB, prepSupMoa, plotGS, sup.moa, wsvd, annotate.gs, GIS, matpower, getmgsa, bootMbpca, distMoa, moGap, softK, mbpca, moaScore, moaCoef, bootMoa ExportMethods: plot, combine, show, print, summary ExportClasses: mgsa, moa, moa.sup Package: monocle Exports: cellPairwiseDistances<-, minSpanningTree<-, reducedDimA<-, BEAM, addCellType, branchTest, buildBranchCellDataSet, calABCs, calILRs, calculateMarkerSpecificity, cellPairwiseDistances, classifyCells, clusterCells, clusterGenes, compareModels, detectBifurcationPoint, detectGenes, differentialGeneTest, dispersionTable, estimate_t, exportCDS, fitModel, genSmoothCurves, get_classic_muscle_markers, importCDS, load_HSMM, load_HSMM_markers, load_lung, markerDiffTable, mcesApply, minSpanningTree, newCellDataSet, newCellTypeHierarchy, orderCells, plot_cell_clusters, plot_cell_trajectory, plot_clusters, plot_complex_cell_trajectory, plot_genes_branched_heatmap, plot_genes_branched_pseudotime, plot_genes_in_pseudotime, plot_genes_jitter, plot_genes_positive_cells, plot_genes_violin, plot_multiple_branches_heatmap, plot_multiple_branches_pseudotime, plot_ordering_genes, plot_pc_variance_explained, plot_pseudotime_heatmap, plot_rho_delta, plot_spanning_tree, reduceDimension, reducedDimA, reducedDimK, reducedDimS, reducedDimW, relative2abs, responseMatrix, selectTopMarkers, setOrderingFilter, vstExprs ExportClasses: CellTypeHierarchy, CellType, CellDataSet Package: MoonlightR Exports: DPA, FEA, GRN, GSEA, LPA, PRA, URA, getDataGEO, getDataTCGA, moonlight, plotCircos, plotFEA, plotNetworkHive, plotURA Package: mosaics Exports: constructBins, readBins, mosaicsFit, mosaicsPeak, mosaicsRunAll, generateWig, mosaicsFitHMM, mosaicsPeakHMM, extractReads, findSummit, adjustBoundary, filterPeak, show, print, plot, estimates, export, bdBin, empFDR, readCoverage, read, seqDepth, postProb, chrID, coord, tagCount, input, mappability, gcContent Package: MOSim Exports: experimentalDesign, mosim, omicData, omicResults, omicSettings, omicSim, plotProfile ExportClasses: SimmiRNAseq, SimTF, SimRNAseq, SimMethylseq, SimDNaseseq, SimChIPseq, MOSimulatorRegion, MOSimulator, MOSimulation Package: motifbreakR Exports: calculatePvalue, motifbreakR, plotMB, snps.from.file, snps.from.rsid, variants.from.file Package: motifcounter Exports: motifEnrichment, motifHitProfile, motifHits, motifcounterOptions, normalizeMotif, readBackground, scoreDist, scoreHistogram, scoreProfile, scoreSequence Package: MotifDb Exports: MotifDb ExportMethods: subset, export, show, query, motifToGene, geneToMotif, associateTranscriptionFactors ExportClasses: MotifList Package: motifmatchr Exports: matchMotifs, match_motifs, motifCounts, motifMatches, motifScores, motif_counts, motif_matches, motif_scores, pwmType ExportMethods: motifScores, motifMatches, motifCounts, matchMotifs Package: motifRG Exports: findMotif, findMotifFasta, findMotifFgBg, summaryMotif, plotMotif, motifLatexTable, motifHtmlTable, refinePWMMotif, refinePWMMotifExtend, getSequence Package: motifStack Exports: browseMotifs, browseMotifsOutput, plotMotifLogo, plotMotifLogoA, plotAffinityLogo, plotXaxis, plotYaxis, colorset, highlightCol, importMatrix, mergeMotifs, motifStack, motifGrob, geom_motif, GeomMotif, plotMotifOverMotif, plotMotifLogoStack, plotMotifLogoStackWithTree, DNAmotifAlignment, plotMotifStackWithPhylog, plotMotifStackWithRadialPhylog, pfm2pwm, motifSignature, motifCloud, motifCircos, motifPiles, readPCM, renderbrowseMotifs, reorderUPGMAtree, getRankedUniqueMotifs ExportMethods: getIC, matrixReverseComplement, addBlank, pcm2pfm, signatures, frequence, nodelist, plot, sigColor, trimMotif, $, $<-, format, as.data.frame ExportClasses: pfm, pcm, psam, ouNode, motifSig, marker Package: MotIV Exports: motifMatch, generateDBScores, readDBScores, writeDBScores, getGademPWM, readGademPWMFile, readPWMfile, viewAlignments, summary, plot, split, filter, makePWM, setFilter, combineMotifs, trimPWMedge, exportAsRangedData, exportAsGRanges, similarity, viewMotifs, occurences, cooccurences, getPWM, nMotifs, motifDistances, motifHclust, motifCutree ExportMethods: show, summary, plot, as.data.frame, combineMotifs, filter, split, exportAsTransfacFile, getPWM ExportClasses: motiv, matches, alignments, transcriptionFactor, filter Package: MPFE Exports: estimatePatterns, plotPatterns, patternMap Package: mpra Exports: MPRASet, getRNA, getDNA, getBarcode, getEid, getEseq, mpralm, get_precision_weights, compute_logratio, normalize_counts ExportMethods: show ExportClasses: MPRASet Package: MPRAnalyze Exports: MpraObject, analyzeComparative, analyzeQuantification, estimateDepthFactors, getAlpha, getDistrParam_DNA, getDistrParam_RNA, getFits_DNA, getFits_RNA, getModelParameters_DNA, getModelParameters_RNA, setDepthFactors, setModel, simulateMPRA, testCoefficient, testEmpirical, testLrt ExportMethods: rnaDepth, rnaCounts, rnaAnnot, model, dnaDepth, dnaCounts, dnaAnnot, controls, MpraObject Package: msa Exports: msa, msaMuscle, msaClustalW, msaClustalOmega, msaPrettyPrint, msaConvert, msaCheckNames ExportMethods: params, version, show, print, msaConservationScore, msaConsensusSequence ExportClasses: MsaDNAMultipleAlignment, MsaRNAMultipleAlignment, MsaAAMultipleAlignment, MsaMetaData Package: msgbsR Exports: checkCuts, diffMeth, plotCircos, plotCounts, rawCounts Package: MSGFgui Exports: MSGFgui, currentData Package: MSGFplus Exports: chargeRange<-, db<-, enzyme<-, fragmentation<-, instrument<-, isotopeError<-, lengthRange<-, matches<-, mods<-, nMod<-, ntt<-, protocol<-, tda<-, tolerance<-, toleranceRange<-, toleranceUnit<-, chargeRange, db, enzyme, finished, fragmentation, getMSGFpar, import, instrument, isotopeError, lengthRange, matches, mods, msgfPar, msgfParChargeRange, msgfParEnzyme, msgfParFragmentation, msgfParFromID, msgfParGUI, msgfParInstrument, msgfParIsotopeError, msgfParLengthRange, msgfParMatches, msgfParModification, msgfParModificationList, msgfParNtt, msgfParProtocol, msgfParTda, msgfParTolerance, nMod, ntt, protocol, runMSGF, running, tda, tolerance, toleranceRange, toleranceUnit ExportClasses: msgfPar Package: msmsEDA Exports: pp.msms.data, gene.table, count.stats, counts.pca, counts.hc, norm.counts, counts.heatmap, disp.estimates, filter.flags, spc.barplots, spc.boxplots, spc.densityplots, spc.scatterplot, batch.neutralize Package: msmsTests Exports: msms.glm.pois, msms.glm.qlll, msms.edgeR, test.results, pval.by.fc, res.volcanoplot Package: MSnbase Exports: MSnSet, abstract, compareMSnSets, defaultNeutralLoss, readMgfData, readMSData, readMSData2, readMSnSet, readMSnSet2, readMzIdData, getEcols, grepEcols, formatRt, fillUp, naplot, makeNaData, makeNaData2, whichNA, extractPrecSpectra, as.matrix.FoICollection, as.data.frame.mzRident, as.data.frame.Spectrum, as.data.frame.MSnSet, ms2df, as.ExpressionSet.MSnSet, as.MSnSet.ExpressionSet, as.MIAME.MIAPE, as.MSnExp.OnDiskMSnExp, as.data.frame.MSnExp, is.na.MSnSet, droplevels.MSnSet, nFeatures, aggvar, nQuants, featureCV, getRatios, makeImpuritiesMatrix, precSelection, precSelectionTable, t.MSnSet, updateFvarLabels, updateFeatureNames, updateSampleNames, normalise, imputeMethods, get.amino.acids, get.atomic.mass, listOf, npcv, selectFeatureData, averageMSnSet, commonFeatureNames, MSmap, MSnSetList, msnsets, objlog, image2, MzTab, smallMolecules, comments, mzTabMode, mzTabType, readMzTabData, writeMzTabData, readMzTabData_v0.9, makeMTD, makePEP, makePRT, ProcessingStep, validateOnDiskMSnExp, MSnbaseOptions, isMSnbaseVerbose, setMSnbaseVerbose, setMSnbaseParallelThresh, isMSnbaseFastLoad, setMSnbaseFastLoad, executeProcessingStep, aggregationFun, Chromatogram, Chromatograms, factorsAsStrings, makeCamelCase, filterIdentificationDataFrame, isCentroidedFromFile, requiredFvarLabels, addMSnSetMetadata, readSRMData, meanMzInts, consensusSpectrum, combineSpectraMovingWindow, estimateMzScattering, hasSpectra, hasChromatograms, mergeFeatureVars, expandFeatureVars, Spectra ExportMethods: updateObject, exprs, assayData, assayData<-, coerce, show, [, [[, [<-, fvarLabels, fData, fData<-, featureNames, featureNames<-, sampleNames, sampleNames<-, fileNames, msInfo, expemail, exptitle, ionSource, ionSourceDetails, analyser, analyzer, analyserDetails, analyzerDetails, detectorType, instrumentModel, instrumentManufacturer, instrumentCustomisations, qual, length, lengths, all.equal, image, plot, plot2d, plotDensity, plotMzDelta, plotNA, MAplot, spectra, processingData, peaksCount, isEmpty, bin, calculateFragments, clean, compareSpectra, estimateNoise, pickPeaks, removePeaks, removeReporters, smooth, addIdentificationData, removeNoId, removeMultipleAssignment, idSummary, intensity, mz, tic, bpi, ionCount, fromFile, centroided, centroided<-, isCentroided, smoothed, smoothed<-, precursorMz, precursorIntensity, precursorCharge, precScanNum, acquisitionNum, scanIndex, rtime, msLevel, collisionEnergy, polarity, trimMz, quantify, purityCorrect, header, dim, multiplex, multiLabels, width, reporterColours, reporterColors, reporterNames, reporterNames<-, writeMgfData, write.exprs, combine, experimentData<-, normalize, scale, log, trimws, exprsToRatios, impute, topN, filterNA, filterZero, filterMsLevel, filterMz, filterPolarity, filterRt, filterFile, filterAcquisitionNum, filterEmptySpectra, filterPrecursorScan, spectrapply, splitByFile, combineFeatures, FeaturesOfInterest, foi, description, FoICollection, addFeaturesOfInterest, rmFeaturesOfInterest, fnamesIn, compfnames, common, unique1, unique2, names, names<-, mzRes, plot3D, msMap, fileName, t, split, metadata, psms, pData, pData<-, $, $<-, phenoData, phenoData<-, chromatogram, colnames<-, reduce, writeMSData, productMz, estimateMzResolution, combineSpectra, isolationWindowLowerMz, isolationWindowUpperMz, filterPrecursorMz, filterIsolationWindow ExportClasses: pSet, MIAPE, MSnExp, MSnProcess, MSnSet, MSnSetList, Spectrum, Spectrum1, Spectrum2, ReporterIons, FeaturesOfInterest, FoICollection, FeatComp, MSmap, MzTab, OnDiskMSnExp, ProcessingStep, Chromatogram, Chromatograms, Spectra Package: MSnID Exports: MSnID, MSnIDFilter ExportMethods: infer_parsimonious_accessions, psms, psms<-, dim, show, names, update, length, as.numeric, $, $<-, [[, [[<-, proteins, accessions, peptides, recalibrate, mass_measurement_error, correct_peak_selection, optimize_filter, id_quality, evaluate_filter, apply_filter, assess_missed_cleavages, assess_termini, read_mzIDs Package: msPurity Exports: Getfiles, assessPuritySingle, averageSpectraSingle, combineAnnotations, createDatabase, create_database, dimsPredictPuritySingle, flag_remove, get_additional_mzml_meta, groupPeaksEx, iwNormGauss, iwNormQE.5, iwNormRcosine, pcalc, purityA, purityD, purityX, spectralMatching, spectral_matching, subtractMZ ExportMethods: writeOut, validate, subtract, show, groupPeaks, getP, frag4feature, filterp, filterFragSpectra, dimsPredictPurity, createMSP, averageSpectra, averageIntraFragSpectra, averageInterFragSpectra, averageAllFragSpectra Package: MSstats Exports: DIAUmpiretoMSstatsFormat, MaxQtoMSstatsFormat, OpenMStoMSstatsFormat, OpenSWATHtoMSstatsFormat, PDtoMSstatsFormat, ProgenesistoMSstatsFormat, SkylinetoMSstatsFormat, SpectronauttoMSstatsFormat, dataProcess, dataProcessPlots, designSampleSize, designSampleSizePlots, groupComparison, groupComparisonPlots, linear_quantlim, modelBasedQCPlots, nonlinear_quantlim, plot_quantlim, quantification Package: MSstatsQC Exports: CUSUMChart, ChangePointEstimator, DataProcess, DecisionMap, MSnbaseToMSstatsQC, MissingDataMap, RadarPlot, RemoveMissing, RiverPlot, XmRChart Package: MSstatsQCgui Exports: RunMSstatsQC Package: MSstatsSampleSize Exports: designSampleSizeClassification, designSampleSizeClassificationPlots, designSampleSizePCAplot, estimateVar, meanSDplot, simulateDataset Package: MSstatsTMT Exports: MaxQtoMSstatsTMTFormat, PDtoMSstatsTMTFormat, SpectroMinetoMSstatsTMTFormat, dataProcessPlotsTMT, groupComparisonTMT, proteinSummarization Package: Mulcom Exports: mulCalc, mulDiff, mulFSG, mulOptPars, mulOptPlot, mulOpt, mulPerm, mulScores, mulCAND, mulDELTA, mulParOpt, mulInt, mulIndex ExportClasses: MULCOM, MULCOM_P Package: MultiAssayExperiment Exports: DataFrame, ExperimentList, MatchedAssayExperiment, MultiAssayExperiment, anyReplicated, experiments, getWithColData, hasAssay, hasRowRanges, intersectColumns, intersectRows, listToMap, longFormat, mapToList, mergeReplicates, prepMultiAssay, replicated, subsetByAssay, subsetByColData, subsetByColumn, subsetByRow, upsetSamples, wideFormat ExportMethods: updateObject, show, sampleMap, replicated, names, metadata, mergeReplicates, length, isEmpty, hasRowRanges, experiments, complete.cases, colData, coerce, assays, assay, anyReplicated, sampleMap<-, names<-, metadata<-, experiments<-, colData<-, [[<-, [[, [<-, $<-, $ ExportClasses: MultiAssayExperiment, MatchedAssayExperiment, ExperimentList Package: multiClust Exports: WriteMatrixToFile, avg_probe_exp, cluster_analysis, input_file, nor.min.max, number_clusters, number_probes, probe_ranking, surv_analysis Package: MultiDataSet Exports: chrNumToChar, createMultiDataSet, create_resultset, getAssociation, lambdaClayton, mae2mds, mds2mae, opt, qq_plot, rowRanges, rowRangesElements, volcano_plot, w_iclusterplus, w_mcia ExportMethods: plot, commonSamples, commonIds, as.list, add_table, add_snps, add_se, add_rse, add_rnaseq, add_methy, add_genexp, add_eset ExportClasses: ResultSet, MultiDataSet Package: multiHiCcompare Exports: MD_composite, MD_hicexp, cyclic_loess, exportJuicebox, fastlo, hic_exactTest, hic_filter, hic_glm, hic_scale, make_hicexp, manhattan_hicexp, perm_test, plot_counts, plot_pvals, pval_heatmap, topDirs ExportMethods: show, results, resolution, normalized, meta, hic_table ExportClasses: Hicexp Package: MultiMed Exports: medTest, medTest.SBMH Package: multiMiR Exports: all_tables, conserved_tables, diseasedrug_tables, get.multimir, get_multimir, list.multimir, list_multimir, multimir_dbCount, multimir_dbInfo, multimir_dbInfoVersions, multimir_dbSchema, multimir_dbTables, multimir_switchDBVersion, predicted_tables, reverse_table_lookup, search.multimir, search_multimir, table_types, tables_wo_target, validated_tables ExportMethods: show, select, keytypes, keys, columns ExportClasses: mmquery_bioc Package: multiOmicsViz Exports: multiOmicsViz, calculateCorForTwoMatrices 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: muscat Exports: aggregateData, calcExprFreqs, mmDS, pbDS, pbHeatmap, pbMDS, prepSCE, prepSim, resDS, simData Package: MutationalPatterns Exports: binomial_test, cluster_signatures, cos_sim, cos_sim_matrix, enrichment_depletion_test, extract_signatures, fit_to_signatures, genomic_distribution, mut_context, mut_matrix, mut_matrix_stranded, mut_strand, mut_type, mut_type_occurrences, mutation_context, mutation_types, mutations_from_vcf, plot_192_profile, plot_96_profile, plot_compare_profiles, plot_contribution, plot_contribution_heatmap, plot_cosine_heatmap, plot_enrichment_depletion, plot_rainfall, plot_signature_strand_bias, plot_spectrum, plot_strand, plot_strand_bias, read_vcfs_as_granges, strand_bias_test, strand_from_vcf, strand_occurrences, type_context 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: MWASTools Exports: MWAS_stats, JBA_binning, JBA_corDistribution, JBA_plotBins, MWAS_KEGG_network, MWAS_heatmap, MWAS_KEGG_pathways, MWAS_KEGG_shortestpaths, MWAS_scatterplotMS, QC_CV_scatterplot, MWAS_SummarizedExperiment, MWAS_filter, CV_filter, MWAS_barplot, MWAS_bootstrapping, MWAS_skylineNMR, plot_spectraNMR, QC_CV, QC_CV_specNMR, QC_PCA, QC_PCA_scoreplot, STOCSY_NMR, MWAS_network Package: mygene Exports: MyGene, getGene, getGenes, query, queryMany, makeTxDbFromMyGene ExportMethods: metadata ExportClasses: MyGene Package: myvariant Exports: MyVariant, getVariant, getVariants, queryVariant, queryVariants, formatHgvs, formatSingleHgvs ExportMethods: metadata ExportClasses: MyVariant Package: mzID Exports: evidence, files, flatten, id, idScanMap, mzID, mzIDCollection, mzIDdatabase, mzIDevidence, mzIDparameters, mzIDpeptides, mzIDpsm, parameters, removeDecoy, software ExportClasses: mzIDCollection, mzID Package: mzR Exports: openMSfile, openIDfile, pwiz.version, nChrom, copyWriteMSData ExportMethods: close, isInitialized, initializeRamp, runInfo, fileName, instrumentInfo, chromatogramsInfo, manufacturer, model, isolationWindow, ionisation, analyzer, detector, header, peaksCount, peaks, spectra, get3Dmap, softwareInfo, sampleInfo, sourceInfo, mzidInfo, psms, modifications, substitutions, database, enzymes, tolerance, score, para, specParams, tic, chromatogram, chromatograms, chromatogramHeader, writeMSData ExportClasses: mzR, mzRramp, mzRnetCDF, mzRpwiz, mzRident Package: NADfinder Exports: IntersectionNotStrict, backgroundCorrection, butterFilter, callPeaks, cumulativePercentage, exportSignals, getCorrelations, groupZscores, log2se, peakdet, plotSig, smoothRatiosByChromosome, tileCount, tileCount2, transformData, trimPeaks, zscoreOverBck Package: NanoStringDiff Exports: createNanoStringSet, createNanoStringSetFromCsv, estNormalizationFactors, glm.LRT, NanoStringDataNormalization, PlotsPositiveHousekeeping ExportMethods: positiveFactor, positiveFactor<-, negativeFactor, negativeFactor<-, housekeepingFactor, housekeepingFactor<-, positiveControl, positiveControl<-, negativeControl, negativeControl<-, housekeepingControl, housekeepingControl<- ExportClasses: NanoStringSet Package: NanoStringQCPro Exports: RccSet, buildCodesetAnnotation, newRccSet, readCdrDesignData, readRcc, readRlf ExportMethods: subtractBackground, presAbsCall, preprocRccSet, posCtrlNorm, makeQCReport, getBlankLabel, getBackground, copyRccSet, contentNorm, checkRccSet, addCodesetAnnotation, RccSet ExportClasses: RccSet Package: nanotatoR Exports: DGV_extraction, Decipher_extraction, buildrunBNBedFiles, clinvar_gene, cohortFrequency, compSmapbed, gene_extraction, gene_list_generation, gtr_gene, internalFrequency, makeMergedSVData, makeMergedSmapData, nanotatoR_main, nonOverlapGenes, omim_gene, overlapGenes, readBNBedFiles, readSMap, run_bionano_filter Package: NBAMSeq Exports: setsf<-, NBAMSeq, NBAMSeqDataSet, getDesign, getsf, makeExample, makeplot, results ExportMethods: getsf, getDesign, setsf<- Package: NBSplice Exports: IsoDataSet, NBSpliceRes, totalGeneCounts ExportMethods: show, results, print, plotVolcano, plotRatiosDisp, plotGeneResults, lowExpIndex, isoGeneRel, isoCounts, initialize, geneCounts, expData, disp, designFormula, contrast, buildLowExpIdx, NBTest, GetGeneResults, GetDSResults, GetDSGenes ExportClasses: NBSpliceRes, IsoDataSet Package: ncdfFlow Exports: as.flowSet, clone.ncdfFlowSet, getFileName, getIndices, initIndices, load_ncfs, ncdfFlowList, ncdfFlowSet, ncfsApply, read.ncdfFlowSet, save_ncfs, unlink, updateIndices ExportMethods: updateIndices, unlink, transform, split, rbind2, phenoData, pData, ncfsApply, ncdfFlowSet, markernames, lapply, keyword, initIndices, getIndices, filter, compensate, colnames, Subset, sampleNames<-, phenoData<-, pData<-, markernames<-, keyword<-, colnames<-, [[<-, [[, [ ExportClasses: ncdfFlowSet, ncdfFlowList Package: ncGTW Exports: adjustRT, compCV, loadProfile, meanCorOl, misalignDetect, ncGTWalign, plotGroup ExportMethods: scanRange, rtncGTW, rtRaw, profiles, ncGTWpeaks, ncGTWpath, groupInfo, downSample, alignData Package: NCIgraph Exports: getNCIPathways, getSubtype.NCIgraph, is.NCIgraph, parseNCInetwork, translateNCI2GeneID ExportClasses: NCIgraph Package: ndexr Exports: ndex_config, ndex_connect, ndex_create_group, ndex_create_network, ndex_create_user, ndex_delete_group, ndex_delete_network, ndex_delete_user, ndex_find_groups, ndex_find_networks, ndex_find_user_byId, ndex_find_user_byName, ndex_find_users, ndex_get_group, ndex_get_network, ndex_group_delete_membership, ndex_group_list_networks, ndex_group_list_users, ndex_group_network_get_permission, ndex_group_set_membership, ndex_network_aspect_get_metadata, ndex_network_delete_permission, ndex_network_get_aspect, ndex_network_get_metadata, ndex_network_get_permission, ndex_network_get_provenance, ndex_network_get_summary, ndex_network_set_systemProperties, ndex_network_update_aspect, ndex_network_update_permission, ndex_network_update_profile, ndex_update_group, ndex_update_network, ndex_update_user, ndex_user_change_password, ndex_user_forgot_password, ndex_user_get_networksummary, ndex_user_get_showcase, ndex_user_list_groups, ndex_user_list_permissions, ndex_user_mail_password, ndex_user_show_group, ndex_user_show_permission, ndex_verify_user, ngraph_fromRCX, ngraph_toRCX, rcx_asNewNetwork, rcx_fromJSON, rcx_fromRCXgraph, rcx_new, rcx_toJSON, rcx_toNGraph, rcx_toRCXgraph, rcx_updateMetaData, rcxgraph_fromRCX, rcxgraph_toRCX Package: NeighborNet Exports: neighborNet Package: netbiov Exports: plot.modules, splitg.mst, mst.plot, mst.plot.mod, plot.spiral.graph, plot.abstract.module, plot.abstract.nodes, level.plot, plot.NetworkSperical.startSet, plot.NetworkSperical, plot.netbiov Package: netboost Exports: cut_trees, mcupgma_exec, nb_clust, nb_dist, nb_filter, nb_mcupgma, nb_moduleEigengenes, nb_plot_dendro, nb_summary, nb_transfer, netboost, tree_search Package: netboxr Exports: geneConnector, globalNullModel, localNullModel, networkSimplify Package: nethet Exports: aggpval, bwprun_mixglasso, diffnet_multisplit, diffnet_singlesplit, diffregr_multisplit, diffregr_singlesplit, dot_plot, export_network, generate_2networks, generate_inv_cov, ggmgsa_multisplit, gsea.iriz, het_cv_glasso, invcov2parcor, invcov2parcor_array, logratio, mixglasso, plot_2networks, scatter_plot, screen_aic.glasso, screen_bic.glasso, screen_cv.glasso, screen_cv1se.lasso, screen_cvfix.lasso, screen_cvmin.lasso, screen_cvsqrt.lasso, screen_cvtrunc.lasso, screen_mb, sim_mix, sim_mix_networks Package: NetPathMiner Exports: KGML2igraph, NPMdefaults, SBML2igraph, assignEdgeWeights, biopax2igraph, colorVertexByAttr, expandComplexes, extractPathNetwork, fetchAttribute, getAttrNames, getAttrStatus, getAttribute, getGeneSetNetworks, getGeneSets, getPathsAsEIDs, layoutVertexByAttr, makeGeneNetwork, makeMetaboliteNetwork, makeReactionNetwork, pathClassifier, pathCluster, pathRanker, pathsToBinary, plotAllNetworks, plotClassifierROC, plotClusterMatrix, plotClusterProbs, plotClusters, plotCytoscapeGML, plotNetwork, plotPathClassifier, plotPathCluster, plotPaths, predictPathClassifier, predictPathCluster, registerMemoryErr, reindexNetwork, rmAttribute, rmSmallCompounds, samplePaths, setAttribute, simplifyReactionNetwork, stdAttrNames, toGraphNEL, vertexDeleteReconnect Package: netprioR Exports: ROC, fit, ranks, simulate_labels, simulate_network_random, simulate_network_scalefree, simulate_phenotype, weights ExportMethods: netprioR ExportClasses: netprioR Package: netReg Exports: cv.edgenet, edgenet Package: netresponse Exports: ICMg.combined.sampler, ICMg.get.comp.memberships, ICMg.links.sampler, P.S, P.Sr, P.r.s, P.rS, P.rs.joint, P.rs.joint.individual, P.s.individual, P.s.r, PlotMixture, PlotMixtureBivariate, PlotMixtureMultivariate, PlotMixtureUnivariate, add.ellipse, bic.mixture, bic.mixture.multivariate, bic.mixture.univariate, bic.select.best.mode, centerData, continuous.responses, detect.responses, enrichment.list.factor, enrichment.list.factor.minimal, factor.responses, factor.responses.minimal, find.similar.features, generate.toydata, get.model.parameters, independent.models, list.responses.continuous.multi, list.responses.continuous.single, list.responses.factor, list.responses.factor.minimal, list.significant.responses, listify.groupings, mixture.model, model.stats, order.responses, pick.model.pairs, pick.model.parameters, plot_data, plot_expression, plot_matrix, plot_response, plot_responses, plot_scale, plot_subnet, read.sif, response.enrichment, response2sample, sample2response, set.breaks, vdp.mixt, vectorize.groupings, write.netresponse.results ExportMethods: get.subnets, get.dat Package: NetSAM Exports: NetSAM Package: netSmooth ExportMethods: robustClusters, pickDimReduction, netSmooth Package: networkBMA Exports: networkBMA, summary.networkBMA, iBMAcontrolLM, iterateBMAlm, varord, contabs, contabs.prelim, contabs.netwBMA, matrixFormat, scores, prc, roc, writeEdges, ScanBMAcontrol, gControl, ScanBMA, fastBMAcontrol, fastgControl Package: ngsReports Exports: FastqcData, FastqcDataList, estGcDistn, fqName, gcAvail, getGC, importNgsLogs, isCompressed, mData, maxAdapterContent, overRep2Fasta, plotAdapterContent, plotAlignmentSummary, plotAssemblyStats, plotBaseQuals, plotDupLevels, plotFastqcPCA, plotGcContent, plotKmers, plotNContent, plotOverrep, plotReadTotals, plotSeqContent, plotSeqLengthDistn, plotSeqQuals, plotSummary, pwf, readTotals, runFastQC, writeHtmlReport ExportMethods: setColours, setAlpha, runFastQC, plotSummary, plotSeqQuals, plotSeqLengthDistn, plotSeqContent, plotReadTotals, plotOverrep, plotNContent, plotKmers, plotGcContent, plotFastqcPCA, plotDupLevels, plotBaseQuals, plotAdapterContent, path, overRep2Fasta, mData, getSummary, getModule, getGC, getColours, gcAvail, fqcVersion, fqName, estGcDistn, [ Package: nnNorm Exports: maNormNN, detectSpatialBias, compNorm Package: NOISeq Exports: noiseq, noiseqbio, readData, addData, dat, rpkm, tmm, uqua, degenes, DE.plot, filtered.data, QCreport, ARSyNseq, PCA.GENES ExportMethods: show, explo.plot, dat2save ExportClasses: Output, Biodetection, CD, CountsBio, GCbias, lengthbias, Saturation, PCA Package: nondetects Exports: qpcrImpute Package: normalize450K Exports: read450K, normalize450K, dont_normalize450K, estimateLC Package: NormalyzerDE Exports: NormalyzerEvaluationResults, NormalyzerResults, NormalyzerStatistics, analyzeNormalizations, calculateContrasts, generateAnnotatedMatrix, generatePlots, generateStatsReport, getRTNormalizedMatrix, getSmoothedRTNormalizedMatrix, getVerifiedNormalyzerObject, globalIntensityNormalization, meanNormalization, medianNormalization, normMethods, normalyzer, normalyzerDE, performCyclicLoessNormalization, performGlobalRLRNormalization, performQuantileNormalization, performSMADNormalization, performVSNNormalization, reduceTechnicalReplicates, setupJobDir, setupRawContrastObject, setupRawDataObject, setupTestData, writeNormalizedDatasets Package: NormqPCR Exports: geomMean, stabMeasureM, stabMeasureRho, selectHKs, deltaCt, deltaCq, replaceNAs, deltaDeltaCt, deltaDeltaCq, makeAllNAs, makeAllNewVal, combineTechReps, combineTechRepsWithSD, replaceAboveCutOff, CqValues, ComputeNRQs Package: normr Exports: diffR, enrichR, exportR, getClasses, getCounts, getEnrichment, getPosteriors, getPvalues, getQvalues, getRanges, regimeR ExportMethods: summary, show, regimeR, print, plot, length, getRanges, getQvalues, getPvalues, getPosteriors, getFilter, getEnrichment, getCounts, getClasses, exportR, enrichR, diffR, countConfigSingleEnd, countConfigPairedEnd ExportClasses: NormRFit, NormRCountConfig Package: npGSEA Exports: getIncidence, npGSEA ExportMethods: geneSetName, stat, sigmaSq, pValues, pTwoSided, pLeft, pRight, xSet, npGSEAPlot, zStat, betaStat, alphaValue, betaValue, chiSqStat, DF, show, betaHats ExportClasses: npGSEAResultNorm, npGSEAResultNormCollection, npGSEAResultBeta, npGSEAResultBetaCollection, npGSEAResultChiSq, npGSEAResultChiSqCollection Package: NTW Exports: P.preestimation, NTW, AP.estimation.Srow, A.estimation.Srow, backward, forward, method.geo, method.sse, method.ml, comb.matrix Package: nucleoSim Exports: syntheticNucMapFromDist, syntheticNucReadsFromDist, syntheticNucReadsFromMap Package: nucleR Exports: controlCorrection, coverage.rpm, export.bed, export.wig, filterFFT, fragmentLenDetect, mergeCalls, pcKeepCompDetect, peakDetection, peakScoring, plotPeaks, processReads, processTilingArray, readBAM, readBowtie, syntheticNucMap Package: nuCpos Exports: predNuCpos, HBA, localHBA, mutNuCpos Package: NuPoP Exports: predNuPoP, readNuPoP, plotNuPoP Package: occugene Exports: checkFormat, delta0, eMult, etDelta, fCumul, fFit, occup2Negenes, unbiasB0, unbiasDelta0, varMult Package: OCplus Exports: approx2d, average.fdr, brk2mid, CDF, CDF.paired, CDFmix, CDFmix.paired, df2var, dgfree, dmt, dmt.paired, dmtmix, dmtmix.paired, DoConstrain, DrawContourlines, EOC, FDR, FDR.paired, fdr1d, fdr2d, FDRp, gausei, lfdr, lfdr.paired, MAsim, MAsim.real, MAsim.smyth, MAsim.var, MidBreaks, MidBreaks.t, OCshow, p0, PermNull, plot.FDR.result, plot.fdr1d.result, plot.fdr2d.result, Rinv, rmatrix, samplesize, smooth1d, smooth2d.basic, smooth2d.direct, summary.fdr.result, tMixture, TOC, topDE, Tornadoplot, tstatistics, Volcanoplot Package: OGSA Exports: copaInt, copaIntE, copaStat, expressionSetDataSet, expressionSetPheno, outCallRank, outCallRankE, outCallTib, outCallTibE, outCount, outMap, outRank, testGScogps 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: OmaDB Exports: annotateSequence, formatTopGO, getAnnotation, getAttribute, getData, getGenome, getGenomeAlignment, getGenomePairs, getHOG, getLocus, getOMAGroup, getObjectAttributes, getProtein, getTaxonomy, getTopGO, getTree, getVersion, getXref, mapSequence, resolveURL, searchProtein, setAPI Package: omicade4 Exports: mcia, plot.mcia, plotVar, selectVar, topVar Package: OmicCircos Exports: circos, segAnglePo, sim.circos Package: omicRexposome Exports: add_cls, add_exp, association, crossomics, getIntegration, plotAssociation, plotHits, plotIntegration, plotLambda, tableHits, tableLambda Package: OmicsLonDA Exports: adjustBaseline, curveFitting, findSigInterval, omicslonda, permutationMC, testStat, testStatPermutation, visualizeArea, visualizeFeature, visualizeFeatureSpline, visualizeTestStatHistogram Package: OmicsMarkeR Exports: RPT, aggregation, canberra, canberra_stability, create.corr.matrix, create.discr.matrix, create.random.matrix, denovo.grid, feature.table, fit.only.model, fs.ensembl.stability, fs.stability, jaccard, kuncheva, modelList, ochiai, optimize.model, pairwise.model.stability, pairwise.stability, params, performance.metrics, perm.class, perm.features, pof, predictNewClasses, sorensen, spearman, svmrfeFeatureRanking, svmrfeFeatureRankingForMulticlass Package: omicsPrint Exports: alleleSharing, beta2genotype, inferRelations Package: OmnipathR Exports: get_annotation_databases, get_complex_genes, get_complexes_databases, get_interaction_databases, get_intercell_categories, get_ptms_databases, get_signed_ptms, import_AllInteractions, import_KinaseExtra_Interactions, import_LigrecExtra_Interactions, import_Omnipath_Interactions, import_Omnipath_PTMS, import_Omnipath_annotations, import_Omnipath_complexes, import_Omnipath_intercell, import_PathwayExtra_Interactions, import_TFregulons_Interactions, import_miRNAtarget_Interactions, interaction_graph, printPath_es, printPath_vs, print_interactions, ptms_graph Package: Onassis Exports: CMdictionary, CMoptions, EntityFinder, Onassis, Similarity, connectToGEODB, dictTypes, experiment_types, filterTerms, findHealthy, getGEOMetadata, listCMOptions, listSimilarities, organism_types ExportMethods: typeSystemRef, similarityInstance, simil, sim, scores, samplesim, paramValueIndex, pairwiseConfigRef, pairwiseConfig, pairsim, ontology, multisim, mergeonassis, icConfig, groupwiseConfigRef, groupsim, groupConfig, findEntities, filterconcepts, entities, dictionary, dict_location, dictRef, dictInfo, compare, collapse, annotateDF, annotate, SynonymType, StopWords, Stemmer, SearchStrategy, OrderIndependentLookup, FindAllMatches, CaseMatch, typeSystemRef<-, similarityInstance<-, simil<-, scores<-, paramValueIndex<-, pairwiseConfigRef<-, pairwiseConfig<-, ontology<-, icConfig<-, groupwiseConfigRef<-, groupConfig<-, entities<-, dictionary<-, dict_location<-, dictRef<-, dictInfo<-, SynonymType<-, StopWords<-, Stemmer<-, SearchStrategy<-, OrderIndependentLookup<-, FindAllMatches<-, CaseMatch<- ExportClasses: Similarity, Onassis Package: oncomix Exports: mixModelParams, oncoMixBimodal, oncoMixIdeal, oncoMixTraditionalDE, plotGeneHist, scatterMixPlot, toMatrix, topGeneQuants Package: OncoScore Exports: combine.query.results, compute.oncoscore, compute.oncoscore.from.region, compute.oncoscore.timeseries, get.genes.from.biomart, perform.query, perform.query.from.region, perform.query.timeseries, plot.oncoscore, plot.oncoscore.timeseries Package: OncoSimulR Exports: oncoSimulPop, oncoSimulIndiv, samplePop, plotPoset, oncoSimulSample, allFitnessEffects, evalGenotype, evalAllGenotypes, simOGraph, plotClonePhylog, OncoSimulWide2Long, allMutatorEffects, evalAllGenotypesMut, evalGenotypeMut, evalGenotypeFitAndMut, evalAllGenotypesFitAndMut, rfitness, plotFitnessLandscape, to_Magellan, Magellan_stats, sampledGenotypes, POM, LOD, diversityPOM, diversityLOD Package: oneSENSE Exports: OneSmapperFreq1, OneSmapperFreq2, getCoords, getParameters, oneSENSE_GUI Package: onlineFDR Exports: ADDIS, ADDIS_spending, Alpha_investing, Alpha_spending, LOND, LONDstar, LORD, LORDdep, LORDstar, SAFFRON, SAFFRONstar, bonfInfinite, online_fallback Package: ontoProc Exports: CLfeats, cellTypeToGO, cellTypeToGenes, children_TAG, cleanCLOnames, ctmarks, cyclicSigset, demoApp, dropStop, fastGrep, getCellLineOnto, getCellOnto, getCellosaurusOnto, getChebiLite, getChebiOnto, getDiseaseOnto, getEFOOnto, getGeneOnto, getHCAOnto, getLeavesFromTerm, getOncotreeOnto, getPATOnto, getPROnto, getUBERON_NE, improveNodes, label_TAG, ldfToTerms, liberalMap, makeSelectInput, make_graphNEL_from_ontology_plot, mapOneNaive, nomenCheckup, onto_plot2, onto_roots, recognizedPredicates, secLevGen, selectFromMap, seur3kTab, siblings_TAG, sym2CellOnto ExportMethods: show, c ExportClasses: TermSet Package: openCyto Exports: add_pop, add_pop_init, cytokine, delete.helperGates, flowClust.1d, flowClust.2d, gate_flowClust_1d, gate_flowClust_2d, gate_flowclust_1d, gate_flowclust_2d, gate_mindensity, gate_mindensity2, gate_quad_sequential, gate_quad_tmix, gate_quantile, gate_tail, gate_tautstring, gating, gatingTemplate, get.helperGates, gh_generate_template, gs_add_gating_method, gs_add_gating_method_init, gs_remove_gating_method, gt_delete_helpergates, gt_gating, gt_get_children, gt_get_gate, gt_get_helpergates, gt_get_nodes, gt_get_parent, gt_toggle_helpergates, listgtMethods, mindensity2, prior_flowClust, prior_flowclust, quadGate.seq, quadGate.tmix, quantileGate, registerPlugins, register_plugins, remove_pop, tautString, tautStringGate, tautstring, templateGen, toggle.helperGates ExportMethods: show, plot, getParent, getNodes, getGate, getChildren ExportClasses: gatingTemplate Package: openPrimeR Exports: Primers, Templates, adjust_binding_regions, assign_binding_regions, check_constraints, check_restriction_sites, classify_design_problem, create_coverage_xls, create_report, design_primers, filter_primers, get_comparison_table, get_cvg_ratio, get_cvg_stats, get_cvg_stats_primer, get_initial_primers, parallel_setup, plot_conservation, plot_constraint, plot_constraint_deviation, plot_constraint_fulfillment, plot_cvg_constraints, plot_cvg_vs_set_size, plot_penalty_vs_set_size, plot_primer, plot_primer_binding_regions, plot_primer_cvg, plot_primer_subsets, plot_template_cvg, primer_significance, read_primers, read_settings, read_templates, runTutorial, score_conservation, score_degen, score_primers, select_regions_by_conservation, subset_primer_set, update_template_cvg, write_primers, write_settings, write_templates ExportMethods: rbind2, cvg_constraints, constraints, constraintLimits, conOptions, cbind2, PCR, cvg_constraints<-, constraints<-, constraintLimits<-, conOptions<-, [, PCR<-, $<- ExportClasses: Templates, Primers, PCR_Conditions, DesignSettings, CoverageConstraints, ConstraintSettings, ConstraintOptions Package: openPrimeRui Exports: startApp Package: oppar Exports: getSampleOutlier, getSubtypeProbes, gsva, opa ExportMethods: show, opa, gsva, getSubtypeProbes, getSampleOutlier, $ ExportClasses: OPPARList Package: oppti Exports: artImpute, clusterData, dropMarkers, dysReg, markOut, plotDen, rankPerOut, statTest, oppti, outScores Package: OPWeight Exports: opw, prob_rank_givenEffect, prob_rank_givenEffect_approx, prob_rank_givenEffect_exact, prob_rank_givenEffect_simu, weight_binary, weight_by_delta, weight_continuous Package: ORFik Exports: assignTSSByCage, bamVarName, computeFeatures, convertToOneBasedRanges, coverageHeatMap, coveragePerTiling, coverageScorings, create.experiment, defineTrailer, detectRibosomeShifts, disengagementScore, distToCds, distToTSS, entropy, extendLeaders, extendTrailers, filterTranscripts, findMapORFs, findORFs, findORFsFasta, findUORFs, firstEndPerGroup, firstExonPerGroup, firstStartPerGroup, floss, fpkm, fractionLength, fread.bed, gcContent, groupGRangesBy, initiationScore, insideOutsideORF, isInFrame, isOverlapping, kozakHeatmap, kozakSequenceScore, lastExonEndPerGroup, lastExonPerGroup, lastExonStartPerGroup, loadRegion, loadTxdb, longestORFs, makeORFNames, metaWindow, numExonsPerGroup, orfScore, outputLibs, overlapsToCoverage, pSitePlot, pmapFromTranscriptF, rankOrder, read.experiment, readBam, readWidths, reassignTSSbyCage, reassignTxDbByCage, reduceKeepAttr, ribosomeReleaseScore, ribosomeStallingScore, scaledWindowPositions, seqnamesPerGroup, shiftFootprints, sortPerGroup, startCodons, startDefinition, startRegion, startRegionString, startSites, stopCodons, stopDefinition, stopSites, strandBool, strandPerGroup, subsetToFrame, tile1, translationalEff, txNames, txSeqsFromFa, uORFSearchSpace, uniqueGroups, uniqueOrder, unlistGrl, widthPerGroup, windowCoveragePlot, windowPerGroup, windowPerReadLength ExportMethods: show ExportClasses: experiment Package: Organism.dplyr Exports: AccnumFilter, AliasFilter, CdsChromFilter, CdsIdFilter, CdsNameFilter, CdsStrandFilter, EnsemblFilter, EnsemblprotFilter, EnsembltransFilter, EnzymeFilter, EvidenceFilter, EvidenceallFilter, ExonChromFilter, ExonStrandFilter, FlybaseCgFilter, FlybaseFilter, FlybaseProtFilter, GeneChromFilter, GeneStrandFilter, GoFilter, GoallFilter, IpiFilter, MapFilter, MgiFilter, OmimFilter, OntologyFilter, OntologyallFilter, PfamFilter, PmidFilter, PrositeFilter, RefseqFilter, TxChromFilter, TxStrandFilter, TxTypeFilter, UnigeneFilter, WormbaseFilter, ZfinFilter, cds, cdsBy, cdsBy_tbl, cds_tbl, exons, exonsBy, exonsBy_tbl, exons_tbl, fiveUTRsByTranscript, fiveUTRsByTranscript_tbl, genes, genes_tbl, hg38light, intronsByTranscript, intronsByTranscript_tbl, mm10light, promoters, promoters_tbl, select_tbl, src_organism, src_ucsc, supportedOrganisms, threeUTRsByTranscript, threeUTRsByTranscript_tbl, transcripts, transcriptsBy, transcriptsBy_tbl, transcripts_tbl ExportMethods: supportedFilters, show, seqinfo, select, orgPackageName, mapIds, keytypes, keys, columns ExportClasses: BasicFilter Package: OrganismDbi Exports: getTxDbIfAvailable, TxDb, TxDb<-, resources, selectByRanges, selectRangesById, makeOrganismPackage, makeOrganismDbFromTxDb, makeOrganismDbFromUCSC, makeOrganismDbFromBiomart ExportMethods: columns, keys, keytypes, select, mapIds, transcripts, exons, cds, genes, transcriptsBy, exonsBy, cdsBy, dbconn, dbfile, taxonomyId, metadata, seqinfo, getTxDbIfAvailable, TxDb, TxDb<-, promoters, disjointExons, microRNAs, tRNAs, intronsByTranscript, fiveUTRsByTranscript, threeUTRsByTranscript, extractUpstreamSeqs, isActiveSeq, isActiveSeq<-, asBED, asGFF, distance, mapToTranscripts, selectByRanges, selectRangesById ExportClasses: OrganismDb Package: OSAT Exports: setup.sample, setup.container, create.optimized.setup, create.experiment.setup, optimal.block, optimal.shuffle, get.experiment.setup, QC, map.to.MSA, multi.barplot, multi.chisq.test, IlluminaBeadChip, GenotypingChip, IlluminaBeadChip24Plate, IlluminaBeadChip48Plate, IlluminaBeadChip96Plate, MSA4.plate, BeadChip96ToMSA4MAP, predefined ExportMethods: getLayout, initialize, plot, show, summary, metadata, metadata<-, exclude<- ExportClasses: gArray, gSlide, BeadChip, gPlate, BeadPlate, gAssembly, gContainer, gSample, gExperimentSetup Package: Oscope Exports: AbsCor, NormForSine, SineFun, FormatSineOut, Opt2Shift, SineOptim, PipeR, ImpShift, PipeShiftCDF, scanK, NISFun, CalcMV, OscopeKM, OscopeENI, OscopeSine, FlagCluster, PermuCut Package: OutlierD Exports: OutlierD Package: OUTRIDER Exports: counts<-, normalizationFactors<-, sampleExclusionMask<-, sizeFactors<-, OUTRIDER, OutriderDataSet, aberrant, computeGeneLength, computeLatentSpace, controlForConfounders, counts, dispersions, estimateBestQ, estimateSizeFactors, filterExpression, findEncodingDim, findInjectZscore, fpkm, fpm, getBestQ, makeExampleOutriderDataSet, normalizationFactors, pValue, padj, plotAberrantPerSample, plotCountCorHeatmap, plotCountGeneSampleHeatmap, plotEncDimSearch, plotExpectedVsObservedCounts, plotExpressedGenes, plotExpressionRank, plotFPKM, plotPowerAnalysis, plotQQ, plotVolcano, results, sampleExclusionMask, sizeFactors, theta, zScore ExportMethods: results, plotDispEsts, fit, filterExpression, computeZscores, computePvalues Package: OVESEG Exports: OVESEGtest, OVESEGtstat, OVEtstatPermTopM, nullDistri, patternDistri, postProbNull, pvalueWeightedEst Package: PAA Exports: batchAdjust, batchFilter, batchFilter.anova, diffAnalysis, loadGPR, mMsMatrix, normalizeArrays, plotArray, plotFeatures, plotFeaturesHeatmap, plotFeaturesHeatmap.2, plotMAPlots, plotNormMethods, preselect, printFeatures, pvaluePlot, selectFeatures, shuffleData, volcanoPlot Package: PADOG Exports: compPADOG, filteranot, padog Package: PAIRADISE Exports: PDseDataSet, PDseDataSetFromMat, pairadise, results ExportClasses: PDseDataSet Package: paircompviz Exports: transReduct, hasse, paircomp Package: panelcn.mops Exports: countBamListInGRanges, createResultTable, getWindows, panelcn.mops, plotBoxplot, runPanelcnMops, splitROIs Package: panp Exports: pa.calls Package: PANR Exports: assoScore, cosineSim, cosineDist ExportMethods: permNULL, fitNULL, fitBM, p2SNR, SNR2p, infer, view, summarize, viewLegend, buildPAN, viewPAN, exportPAN, sigModules, pvclustModule, viewNestedModules ExportClasses: BetaMixture, PAN Package: PanVizGenerator Exports: PanVizGenerator, getGO, panviz Package: parglms Exports: parGLM ExportMethods: parGLM Package: parody Exports: calout.detect, mv.calout.detect, hamp.scale.3, tukeyor, box.scale Package: PAST Exports: assign_SNPs_to_genes, find_pathway_significance, load_GWAS_data, load_LD, plot_pathways Package: Path2PPI Exports: homologyScore ExportMethods: addReference, getHybridNetwork, getPPI, plot.Path2PPI, predictPPI, removeReference, showInteraction, showReferences ExportClasses: Path2PPI Package: PathoStat Exports: Bootstrap_LOOCV_LR_AUC, Chisq_Test_Pam, Fisher_Test_Pam, GET_PAM, LOOAUC_simple_multiple_noplot_one_df, LOOAUC_simple_multiple_one_df, TranslateIdToTaxLevel, Wilcox_Test_df, findRAfromCount, findTaxonMat, findTaxonomy, findTaxonomy300, getShinyInput, getShinyInputCombat, getShinyInputOrig, getSignatureFromMultipleGlmnet, grepTid, loadPathoscopeReports, loadPstat, log2CPM, pathostat1, percent, phyloseq_to_edgeR, plotPCAPlotly, plotPCoAPlotly, readPathoscopeData, runPathoStat, savePstat, setShinyInput, setShinyInputCombat, setShinyInputOrig, summarizeTable ExportClasses: PathoStat Package: pathRender Exports: rendercMAPPathway, graphcMAP, pwayRendAttrs, reduceES, plotExGraph, colorNodes ExportMethods: plot ExportClasses: pwayGraph, coloredGraph Package: pathVar Exports: makeDBList, pathVarOneSample, pathVarTwoSamplesCont, sigPway, plotPway, saveAsPDF, getGenes, diagnosticsVarPlots, pathVarTwoSamplesDisc, diagnosticsVarPlotsTwoSample, plotAllTwoSampleDistributionCounts ExportClasses: geneDistributionSet, significantPathway, geneDistributionSet2, significantPathway2, geneSet, geneDistributionSet3, significantPathway3 Package: pathview Exports: download.kegg, node.info, combineKEGGnodes, reaction2edge, node.map, eg2id, id2eg, geneannot.map, cpdkegg2name, cpdname2kegg, cpd2kegg, cpdidmap, kegg.species.code, mol.sum, sim.mol.data, node.color, col.key, wordwrap, strfit, pathview, keggview.native, keggview.graph Package: pathwayPCA Exports: getAssay<-, getEvent<-, getEventTime<-, getPathwayCollection<-, getResponse<-, getSampleIDs<-, AESPCA_pVals, Contains, CreateOmics, CreatePathwayCollection, ExtractAESPCs, LoadOntoPCs, SE2Tidy, SubsetPathwayData, SuperPCA_pVals, TransposeAssay, WhichPathways, getAssay, getEvent, getEventTime, getPathPCLs, getPathpVals, getPathwayCollection, getResponse, getSampleIDs, getTrimPathwayCollection, read_gmt, write_gmt ExportMethods: show ExportClasses: OmicsSurv, OmicsReg, OmicsPathway, OmicsCateg Package: PathwaySplice Exports: .onAttach, gmtGene2Cat, lrTestBias, enrichmentMap, makeGeneTable, compareResults, runPathwaySplice Package: paxtoolsr Exports: addAttributeList, convertDataFrameListsToVectors, convertIds, convertSifToGmt, downloadFile, downloadPc2, downloadSignedPC, fetch, filterSif, getCacheFiles, getErrorMessage, getNeighbors, getPc, getPcDatabaseNames, getPcUrl, getShortestPathSif, getSifInteractionCategories, graphPc, integrateBiopax, loadSifInIgraph, mapAttributes, mapValues, mergeBiopax, pcDirections, pcFormats, pcGraphQueries, processPcRequest, readBiopax, readGmt, readPcPathwaysInfo, readSbgn, readSif, readSifnx, searchListOfVectors, searchPc, splitSifnxByPathway, summarize, summarizeSif, toCytoscape, toGSEA, toLevel3, toSBGN, toSif, toSifnx, topPathways, traverse, validate Package: pcaExplorer Exports: correlatePCs, distro_expr, geneprofiler, genespca, get_annotation, get_annotation_orgdb, hi_loadings, limmaquickpca2go, makeExampleDESeqDataSet_multifac, pair_corr, pca2go, pcaExplorer, pcaplot, pcaplot3d, pcascree, plotPCcorrs, topGOtable Package: pcaMethods Exports: Q2, RnipalsPca, asExprSet, bpca, checkData, cvseg, kEstimate, kEstimateFast, listPcaMethods, llsImpute, nipalsPca, nlpca, nni, pca, plotPcs, ppca, prep, robustPca, robustSvd, showNniRes, showPcaRes, svdImpute, svdPca ExportMethods: wasna, slplot, scores, scl, scaled, sDev, nmissing, nVar, nPcs, nP, nObs, method, loadings, leverage, cvstat, completeObs, centered, center, R2cum, R2VX, DModX ExportClasses: pcaRes, nniRes, nlpcaNet Package: PCAN Exports: calcHpSim, compareHPSets, computeHpIC, hpGeneHeatmap, hpGeneListComp, hpSetCompBestMatch, hpSetCompSummary Package: PCAtools Exports: pca, getComponents, getVars, getLoadings, screeplot, biplot, pairsplot, plotloadings, eigencorplot, findElbowPoint, parallelPCA Package: pcot2 Exports: aveExprs, aveProbe, corplot2, corplot, Cor, geneLocator, getImat, pco, pcot2, plotCor, rb, rg, t2.permu, t2, t2.unequ, wb Package: PCpheno Exports: graphTheory, overlap, complexStatus, buildFDMat, getFDgene, reduceM, densityEstimate, truncName, getDescr, KEGG2SCISI, ppiInteract ExportMethods: hyperGTest, summary, geneCounts, universeCounts, pvalues, oddsRatios, expectedCounts, universeBuilder, categoryToEntrezBuilder, plot ExportClasses: CoHyperGParams, CoHyperGResult, testResult, deResult, gtResult Package: pcxn Exports: pcxn_explore, pcxn_analyze, pcxn_gene_members, pcxn_heatmap, pcxn_network Package: pdInfoBuilder Exports: cdf2table, sequenceParser ExportMethods: chipName, getGeometry, makePdInfoPackage ExportClasses: AffyExpressionPDInfoPkgSeed, AffyTilingPDInfoPkgSeed, AffySNPPDInfoPkgSeed, AffySNPPDInfoPkgSeed2, AffySNPCNVPDInfoPkgSeed, AffySNPCNVPDInfoPkgSeed2, AffyExonPDInfoPkgSeed, AffyGenePDInfoPkgSeed, NgsExpressionPDInfoPkgSeed, NgsTilingPDInfoPkgSeed Package: peakPantheR Exports: peakPantheRAnnotation, peakPantheR_ROIStatistics, peakPantheR_loadAnnotationParamsCSV, peakPantheR_parallelAnnotation, peakPantheR_plotEICFit, peakPantheR_plotPeakwidth, peakPantheR_singleFileSearch ExportMethods: useUROI, useFIR, uROIExist, uROI, spectraMetadata, resetFIR, resetAnnotation, peakTables, peakFit, outputAnnotationResult, outputAnnotationDiagnostic, nbSamples, nbCompounds, isAnnotated, filepath, filename, dataPoints, cpdName, cpdMetadata, cpdID, annotationTable, annotationParamsDiagnostic, annotationDiagnosticPlots, acquisitionTime, TIC, ROI, FIR, EICs Package: PECA Exports: PECA_AffyBatch, PECA_CEL, PECA_tsv, PECA_df, PECASI Package: PepsNMR Exports: Apodization, BaselineCorrection, Bucketing, Draw, DrawPCA, DrawSignal, FirstOrderPhaseCorrection, FourierTransform, GroupDelayCorrection, InternalReferencing, NegativeValuesZeroing, Normalization, PreprocessingChain, ReadFid, ReadFids, RegionRemoval, SolventSuppression, Warping, WindowSelection, ZeroFilling, ZeroOrderPhaseCorrection, ZoneAggregation Package: pepStat Exports: create_db, makeCalls, makePeptideSet, normalizeArray, plotArrayImage, plotArrayResiduals, restab, shinyPepStat, slidingMean, summarizePeptides ExportMethods: width, values, summary, subset, start, show, ranges<-, ranges, position, peptide<-, peptide, pepZscore<-, pepZscore, featureID, end, clade, [ ExportClasses: peptideSet Package: pepXMLTab Exports: pepXML2tab, PSMfilter Package: PERFect Exports: DiffFiltLoss, FL_J, FiltLoss, NC_Order, NCw_Order, NP_Order, PERFect_perm, PERFect_perm_reorder, PERFect_sim, TraditR1, TraditR2, pvals_Order, pvals_Plots Package: perturbatr Exports: bootstrap, dataSet, diffuse, filter, geneEffects, graph, hm, inference, isBootstrapped, modelFit, nestedGeneEffects, params ExportClasses: PerturbationData, NetworkAnalysedPerturbationData, HMAnalysedPerturbationData Package: PGA Exports: dbCreator, reportGear, runTandem, parserGear, easyRun, PrepareAnnotationEnsembl2, PrepareAnnotationRefseq2, createProDB4DenovoRNASeq, addGeneName4Ensembl, buildFusionProteinDB Package: pgca Exports: applyDict, pgcaDict, saveDict Package: PGSEA Exports: .rwb ExportClasses: smc Package: phantasus Exports: getES, getGDS, getGSE, read.gct, reparseCachedESs, servePhantasus, write.gct Package: PharmacoGx Exports: PharmacoSet, amcc, availablePSets, checkPSetStructure, computeABC, computeAUC, computeAmax, computeIC50, computeICn, computeSlope, connectivityScore, cosinePerm, downloadPSet, downloadPertSig, drugDoseResponseCurve, drugPerturbationSig, drugSensitivitySig, filterNoisyCurves, gwc, intersectList, intersectPSet, logLogisticRegression, mDataNames, mcc, showSigAnnot, subsetTo, summarizeMolecularProfiles, summarizeSensitivityProfiles, symSetDiffList, unionList ExportMethods: show, sensitivityProfiles, sensitivityMeasures, sensitivityInfo, sensNumber, phenoInfo, pertNumber, pSetName, molecularProfiles, featureInfo, fNames, drugNames, drugInfo, dim, dateCreated, cellNames, cellInfo, sensitivityProfiles<-, sensitivityInfo<-, sensNumber<-, phenoInfo<-, pertNumber<-, molecularProfiles<-, featureInfo<-, drugNames<-, drugInfo<-, cellNames<-, cellInfo<-, [ Package: phenopath Exports: clvm, interaction_effects, interaction_sds, interactions, phenopath, plot_elbo, significant_interactions, simulate_phenopath, trajectory Package: PhenStat Exports: analysedDataset, checkDataset, PhenList, summaryOutput, testDataset, PhenStatReport, analysisResults, vectorOutput, summaryOutput, qqplotGenotype, boxplotSexGenotype, recommendMethod, plot.PhenList, plot.PhenTestResult, summary.PhenTestResult, columnChecks Package: philr Exports: annotate_balance, buildilrBasep, calculate.blw, clrp, clrpInv, convert_to_long, ilrp, ilrpInv, mean_dist_to_tips, miniclo, name.balance, name.to.nn, named_rtree, nn.to.name, philr, philrInv, phylo2sbp, shiftp, shiftpInv Package: phosphonormalizer Exports: normalizePhospho Package: PhyloProfile Exports: calcPresSpec, checkInputValidity, checkNewick, checkOmaID, clusterDataDend, compareMedianTaxonGroups, compareTaxonGroups, createArchiPlot, createGeneAgePlot, createLongMatrix, createPercentageDistributionData, createProfileFromOma, createRootedTree, createVarDistPlot, createVariableDistributionData, createVariableDistributionDataSubset, dataCustomizedPlot, dataFeatureTaxGroup, dataMainPlot, dataVarDistTaxGroup, estimateGeneAge, fastaParser, featureDistTaxPlot, filterProfileData, fromInputToProfile, geneAgePlotDf, generateSinglePlot, getAllDomainsOma, getAllFastaOma, getCommonAncestor, getCoreGene, getDataClustering, getDataForOneOma, getDendrogram, getDistanceMatrix, getFastaFromFasInput, getFastaFromFile, getFastaFromFolder, getIDsRank, getInputTaxaID, getInputTaxaName, getNameList, getOmaDataForOneOrtholog, getOmaDomainFromURL, getOmaMembers, getQualColForVector, getSelectedFastaOma, getSelectedTaxonNames, getTaxonomyInfo, getTaxonomyMatrix, getTaxonomyRanks, gridArrangeSharedLegend, heatmapPlotting, highlightProfilePlot, mainTaxonomyRank, parseDomainInput, parseInfoProfile, processNcbiTaxonomy, reduceProfile, runPhyloProfile, sortInputTaxa, sortTaxaFromTree, taxonomyTableCreator, varDistTaxPlot, wideToLong, xmlParser Package: phyloseq Exports: otuTable<-, otu_table<-, phy_tree<-, sam_data<-, sampleData<-, sample_data<-, sample_names<-, speciesAreRows<-, taxTab<-, tax_table<-, taxa_are_rows<-, taxa_names<-, tre<-, DPCoA, UniFrac, access, build_tax_table, distance, distanceMethodList, estimate_richness, export_env_file, export_mothur_dist, filter_taxa, filterfunSample, filterfun_sample, gapstat_ord, genefilterSample, genefilter_sample, getSamples, getSpecies, getTaxa, getVariable, get_sample, get_taxa, get_taxa_unique, get_variable, getslots.phyloseq, import, import_RDP_cluster, import_RDP_otu, import_biom, import_env_file, import_mothur, import_mothur_dist, import_pyrotagger_tab, import_qiime, import_qiime_otu_tax, import_qiime_sampleData, import_qiime_sample_data, import_uparse, import_usearch_uc, make_network, merge_phyloseq, merge_phyloseq_pair, merge_samples, merge_species, merge_taxa, microbio_me_qiime, mt, nodeplotblank, nodeplotboot, nodeplotdefault, nsamples, nspecies, ntaxa, ordinate, otuTable, otu_table, parse_taxonomy_default, parse_taxonomy_greengenes, parse_taxonomy_qiime, phy_tree, phyloseq, phyloseq_to_deseq2, phyloseq_to_metagenomeSeq, plot_bar, plot_clusgap, plot_heatmap, plot_net, plot_network, plot_ordination, plot_phyloseq, plot_richness, plot_richness_estimates, plot_scree, plot_taxa_bar, plot_tree, prune_samples, prune_species, prune_taxa, psmelt, rank.names, rank_names, rarefy_even_depth, read_tree, read_tree_greengenes, refseq, rm_outlierf, samData, sam_data, sample.names, sample.variables, sampleData, sampleNames, sampleSums, sample_data, sample_names, sample_sums, sample_variables, show_mothur_cutoffs, show_mothur_list_cutoffs, species.names, speciesAreRows, speciesSums, speciesarerows, subset_ord_plot, subset_samples, subset_species, subset_taxa, t, taxTab, tax_glom, tax_table, taxa_are_rows, taxa_names, taxa_sums, taxaplot, taxglom, taxtab, threshrank, threshrankfun, tip_glom, tipglom, topf, topk, topp, transformSampleCounts, transform_sample_counts, tre, tree_layout ExportMethods: show, [ ExportClasses: taxonomyTable, sample_data, phyloseq, phylo, otu_table, dist Package: Pi Exports: cTarget, dTarget, eGSEA, eTarget, pNode, pPerf, sGS, sTarget, xContour, xCorrelation, xGSEAbarplot, xGSEAconciser, xGSEAdotplot, xGSsimulator, xMLcaret, xMLcompare, xMLdensity, xMLdotplot, xMLfeatureplot, xMLglmnet, xMLparameters, xMLrandomforest, xMLrename, xMLzoom, xPier, xPierABF, xPierABFheatmap, xPierAnno, xPierCor, xPierCross, xPierEvidence, xPierGRs, xPierGSEA, xPierGenes, xPierKEGG, xPierMRS, xPierManhattan, xPierMatrix, xPierPathways, xPierROCR, xPierSNPs, xPierSNPsAdv, xPierSNPsAdvABF, xPierSNPsConsensus, xPierSubnet, xPierTrack, xPierTrackAdv, xPredictCompare, xPredictROCR, xRWR, xVisEvidence, xVisEvidenceAdv Package: piano Exports: loadMAdata, runQC, extractFactors, diffExp, polarPlot, loadGSC, runGSA, GSAsummaryTable, geneSetSummary, networkPlot, consensusScores, consensusHeatmap, runGSAhyper, GSAheatmap, writeFilesForKiwi, exploreGSAres, networkPlot2 Package: pickgene Exports: adjustlevel, chen.poly, chipnorm, dencont, dencum, denlines, do.oddsplot, em.ggb, fitgg, gammaden, holms, lod.ggb, lod.plot, lodprobes, loglik, makecont, model.pickgene, multipickgene, nlminb, nloglik, normal.richmond, npdiag, nploglik, oddsplot, orangene, pickedchisq, pickedhist, pickedpair, pickedscore, pickgene, pickgene.poly, pickgene.two, pickgene2, pmarg, predrecur, rangene, rankgene, robustbox, robustscale, s.check0, s.check1, s.check2, s.marg, shrinkplot, sixden, toprankgene, twoarray.norm, twoarray.plot, twowayanovapickgene Package: PICS Exports: segReadsList, segReadsListPE, segReadsPE, segReadsGeneric, segReads, segmentPICS, summarySeg, makeRangedDataOutput, PICS, picsFDR, newPicsError, setParaEM, setParaPrior, candidate.region, segChrRead, bam2gr ExportMethods: coerce, show, summary, plot, wigDensity, chromosome, score, se, seF, seR, sigmaSqF, sigmaSqR, mu, delta, w, code, length, K, [, [[, map, minRange, maxRange, scoreForward, scoreReverse ExportClasses: segReads, segReadsList, segReadsPE, segReadsListPE, pics, picsError, picsList Package: Pigengene Exports: one.step.pigengene, check.pigengene.input, balance, calculate.beta, wgcna.one.step, compute.pigengene, plot.pigengene, pheatmap.type, project.eigen, learn.bn, draw.bn, make.decision.tree, get.used.features, get.fitted.leaf, module.heatmap, compact.tree, get.genes, preds.at, pvalues.manova, gene.mapping, dcor.matrix, check.nas, combine.networks, save.if, message.if ExportClasses: pigengene Package: PING Exports: PING, postPING, newPingError, segReads, segReadsPE, segReadsList, segReadsListPE, segmentPING, NucleosomeTrack, CoverageTrack, RawReadsTrack, plotSummary, makeRangedDataOutput, setParaPrior, setParaEM, bam2gr ExportMethods: show, summary, plot, se, seF, seR, sigmaSqF, sigmaSqR, mu, delta, w, code, length, K, [, [[, as.data.frame, chromosome, score, density ExportClasses: ping, pingError, pingList Package: pipeFrame Exports: Step, addEdges, checkAndInstallBSgenome, checkAndInstallGenomeFa, checkAndInstallOrgDb, checkAndInstallTxDb, checkFileCreatable, checkFileExist, checkPathExist, genReport, getBasenamePrefix, getGenome, getJobDir, getJobName, getNextSteps, getObjsInPipe, getPathPrefix, getPipeName, getPrevSteps, getRef, getRefDir, getRefFiles, getRefRc, getThreads, getTmpDir, getValidGenome, initPipeFrame, printMap, processing, runWithFinishCheck, setGenome, setJobName, setPipeName, setRefDir, setThreads, setTmpDir ExportMethods: writeLog, stepType, stepName, stepID, report, property, pipeName, param, output, isReady, input, init, getStepWorkDir, getParamMD5Path, getParamItems, getParam, getAutoPath, clearStepCache, checkRequireParam, checkAllPath, argv, report<-, property<-, param<-, output<-, input<-, $<-, $ Package: pkgDepTools Exports: getInstallOrder, makeDepGraph Package: plethy Exports: makeBuxcoDB, annoTable, annoCols, annoLevels, dbName, samples, variables, tables, retrieveData, addAnnotation, dbImport, summaryMeasures, retrieveMatrix, tsplot, mvtsplot, day.infer.query, break.type.query, parse.buxco, parse.buxco.basic, add.labels.by.sample, adjust.labels, get.err.breaks, proc.sanity, sample.db.path, buxco.sample.data.path ExportClasses: BuxcoDB Package: plier Exports: justPlier Package: plotGrouper Exports: %>%, gplot, organizeData, plotGrouper, readData, readData_example Package: PLPE Exports: lpe.paired, lpe.paired.default, lpe.paired.fdr, lpe.paired.fdr.default, print.lpe.paired, summary.lpe.paired, print.lpe.paired.fdr, summary.lpe.paired.fdr, am.trans.paired, base.error.paired, generate.null Package: plrs Exports: plrs.sim, plrs.cb, plrs.series, criteria, modify.conf, plrs, plrs.select, plrs.test ExportMethods: coef, fitted, effects, knots, model.matrix, plot, predict, print, residuals, show, summary ExportClasses: plrs, plrs.select, plrs.series Package: plw Exports: estimateMVbeta, estimateSigmaMVbeta, estimateSigmaMV, estimateSigma, getKnots, lmw, plw, scaleParameterPlot, topRankSummary, varHistPlot, plotSummaryLog2FC, plotSummaryT, logitTTransform, logitTStat, studenttTTest, madByIndex, meanByIndex, medianByIndex, orderStatByIndex, sdByIndex, meanSdByRow, HowToPLW Package: plyranges Exports: !!!, !!, %>%, %intersect%, %setdiff%, %union%, anchor, anchor_3p, anchor_5p, anchor_center, anchor_centre, anchor_end, anchor_start, arrange, as_granges, as_iranges, as_ranges, between, bind_ranges, chop_by_gaps, chop_by_introns, complement_ranges, complement_ranges_directed, compute_coverage, count_overlaps, count_overlaps_directed, count_overlaps_within, count_overlaps_within_directed, disjoin_ranges, disjoin_ranges_directed, expand_ranges, filter, filter_by_non_overlaps, filter_by_overlaps, find_overlaps, find_overlaps_directed, find_overlaps_within, find_overlaps_within_directed, flank_downstream, flank_left, flank_right, flank_upstream, genome_info, get_genome_info, group_by, group_by_overlaps, group_vars, groups, intersect_ranges, intersect_ranges_directed, interweave, join_follow, join_follow_left, join_follow_upstream, join_nearest, join_nearest_downstream, join_nearest_left, join_nearest_right, join_nearest_upstream, join_overlap_inner, join_overlap_inner_directed, join_overlap_inner_within, join_overlap_inner_within_directed, join_overlap_intersect, join_overlap_intersect_directed, join_overlap_intersect_within, join_overlap_intersect_within_directed, join_overlap_left, join_overlap_left_directed, join_overlap_left_within, join_overlap_left_within_directed, join_overlap_self, join_overlap_self_directed, join_overlap_self_within, join_overlap_self_within_directed, join_precede, join_precede_downstream, join_precede_right, mutate, n, n_distinct, overscope_ranges, pair_follow, pair_nearest, pair_overlaps, pair_precede, read_bam, read_bed, read_bed_graph, read_bigwig, read_gff, read_gff1, read_gff2, read_gff3, read_narrowpeaks, read_wig, reduce_ranges, reduce_ranges_directed, select, set_end, set_genome_info, set_seqnames, set_start, set_strand, set_width, setdiff_ranges, setdiff_ranges_directed, shift_downstream, shift_left, shift_right, shift_upstream, slide_ranges, span, stretch, summarise, summarize, tile_ranges, unanchor, ungroup, union_ranges, union_ranges_directed, write_bed, write_bed_graph, write_bigwig, write_gff, write_gff1, write_gff2, write_gff3, write_narrowpeaks, write_wig ExportClasses: GroupedIntegerRanges, GroupedGenomicRanges, FileOperator, DeferredGenomicRanges, BamFileOperator Package: pmm Exports: hitheatmap, pmm, sharedness Package: podkat Exports: computeKernel, unmaskedRegions, readSampleNamesFromVcfHeader, readRegionsFromBedFile, betaWeights, logisticWeights, invSdWeights ExportMethods: show, summary, print, nullModel, assocTest, p.adjust, variantInfo, MAF, genotypeMatrix, readGenotypeMatrix, readVariantInfo, partitionRegions, filterResult, qqplot, plot, sort, c, [, residuals, coefficients, split, weights, names ExportClasses: NullModel, AssocTestResult, AssocTestResultRanges, VariantInfo, GenotypeMatrix Package: pogos Exports: DRProfSet, DRTraceSet, basicDecoder, compoundsByCell, getDrugs, iriCCLE, rxdbQuery_v1, topEndpoints_v1, traces ExportMethods: plot, [ ExportClasses: DRTraceSet, DRProfile Package: polyester Exports: NB, add_error, add_gc_bias, add_platform_error, count_transcripts, create_read_numbers, fpkm_to_counts, generate_fragments, getAttributeField, get_params, get_reads, reverse_complement, seq_gtf, simulate_experiment, simulate_experiment_countmat, simulate_experiment_empirical, write_reads Package: POST Exports: POSTglm, POSTcoxph Package: PoTRA Exports: PoTRA.corN Package: PowerExplorer Exports: estimatePower, listEstPwr, listPredPwr, plotEstPwr, plotPredPwr, predictPower ExportClasses: PowerExplorerStorage Package: powerTCR Exports: fdiscgammagpd, qdiscgammagpd, rdiscgammagpd, ddiscgammagpd, pdiscgammagpd, fdesponds, get_bootstraps, get_distances, get_diversity, get_nllh, get_mle, JS_desponds, JS_spliced, JS_dist, clusterPlot, parseFile, parseFolder Package: ppiStats Exports: assessSymmetry, bpMatrix, calcInOutDegStats, degreeEstimates, estErrProbMethodOfMoments, estimateCCMErrorRates, findAdjacent, genBPGraph, idHomodimers, idStochastic, idSystematic, idViableProteins, nullDistDoublyTestedEdges, ppiBuildParams4GO, ppiHGTest4GO, ppiBuildParams4PFAM, ppiHGTest4PFAM, twowayPERM, findDegree, makeBinVect, estimatePPIErrorRates, createSummaryTables, viabilityCharts, inOutScatterCharts, separateExptBySize, findAdjacent Package: prada Exports: analysePlate, as.all, barploterrbar, combineFrames, csApply, fitNorm2, getPradaPar, plotNorm2, devDims, plotPlate, readCytoSet, readFCS, read.fcs, removeCensored, setPradaPars, thresholds, threePanelPlot, devRes, .drawCircle, .drawPie, vpLocation, touchFCS, combineGates, progress, updateProgress, killProgress, getAlphaNumeric ExportMethods: colnames, colnames<-, description, description<-, exprs, exprs<-, length, [, [[, [[<-, pData, phenoData, phenoData<-, show, plot, gate, applyGate, drawGate, gate<-, names, names<-, as.gateSet, nrow, ncol, appendGates, lines, split ExportClasses: cytoFrame, cytoSet, gate, gateSet Package: pram Exports: buildModel, defIgRanges, evalModel, prepIgBam, runPRAM, selModel Package: prebs Exports: calc_prebs Package: PrecisionTrialDrawer Exports: showTumorType, showCancerStudy ExportMethods: show, getAlterations, subsetAlterations, panelDesigner, cpArguments, cpData, cpDataSubset, coveragePlot, coverageStackPlot, saturationPlot, coocMutexPlot, survPowerSampleSize, survPowerSampleSize1Arm, cpFreq, panelOptimizer, appendRepo, dataExtractor, propPowerSampleSize, filterMutations, filterFusions ExportClasses: CancerPanel Package: PREDA Exports: GenomicAnnotationsFromLibrary, MergeStatisticAnnotations2DataForPREDA, PREDA_main, preprocessingGE, SODEGIRpreprocessingGE, GenomicAnnotationsFromfile, GenomicAnnotationsFromdataframe, GenomicAnnotationsForPREDAFromfile, DataForPREDAMedianCenter, StatisticsForPREDAFromfile, StatisticsForPREDAFromdataframe, GenomicRegionsFindOverlap, GenomicRegions2dataframe, GenomicRegionsFromfile, GenomicRegionsFromdataframe ExportMethods: GenomicAnnotations2dataframe, GenomicAnnotationsSortAndCleanNA, GenomicAnnotations2reference_positions, GenomicAnnotationsFilter_neg, GenomicAnnotationsFilter_pos, GenomicAnnotationsExtract, GenomicAnnotations2GenomicAnnotationsForPREDA, GenomicAnnotationsForPREDA2GenomicAnnotations, GenomicAnnotationsForPREDA2dataframe, GenomicAnnotationsForPREDA2PREDAResults, StatisticsForPREDA2dataframe, StatisticsForPREDAFilterColumns_neg, StatisticsForPREDAFilterColumns_pos, analysesNames, getStatisticByName, DataForPREDA2dataframe, DataForPREDA2GenomicAnnotationsForPREDA, DataForPREDA2StatisticsForPREDA, PREDAResults2dataframe, PREDAResults2PREDADataAndResults, PREDAResults2GenomicRegionsSingle, PREDAResults2GenomicRegions, PREDAResultsGetObservedFlags, PREDADataAndResults2dataframe, GenomicRegionsChrNumber, GenomicRegionsNumber, GenomicRegionsSpan, GenomicRegionsTotalSpan, GenomicRegionsCreateRegionsIds, GenomicRegionsComparison, GenomicRegionsAnnotate, GenomicRegionsFilter_neg, GenomicRegionsFilter_pos, eset2GenomicAnnotations, statisticsForPREDAfromEset, genomePlot, computeDatasetSignature, SODEGIR_GEstatistics ExportClasses: GenomicAnnotations, GenomicAnnotationsForPREDA, StatisticsForPREDA, DataForPREDA, PREDAResults, PREDADataAndResults, GenomicRegions Package: primirTSS Exports: find_tss, peak_join, peak_merge, plot_primiRNA, run_primirTSSapp, trans_cor Package: PrInCE Exports: PrInCE, adjacency_matrix_from_data_frame, adjacency_matrix_from_list, build_gaussians, calculate_features, calculate_precision, check_gaussians, choose_gaussians, clean_profile, clean_profiles, co_apex, concatenate_features, detect_complexes, filter_profiles, fit_curve, fit_gaussians, impute_neighbors, is_unweighted, is_weighted, make_feature_from_data_frame, make_feature_from_expression, make_initial_conditions, make_labels, match_matrix_dimensions, predict_ensemble, predict_interactions, replace_missing_data, threshold_precision Package: proBAMr Exports: PrepareAnnotationGENCODE, PSMtab2SAM Package: proBatch Exports: adjust_batch_trend_df, adjust_batch_trend_dm, calculate_PVCA, calculate_feature_CV, calculate_peptide_corr_distr, calculate_sample_corr_distr, center_feature_batch_means_df, center_feature_batch_means_dm, center_feature_batch_medians_df, center_feature_batch_medians_dm, check_sample_consistency, correct_batch_effects_df, correct_batch_effects_dm, correct_with_ComBat_df, correct_with_ComBat_dm, create_peptide_annotation, date_to_sample_order, dates_to_posix, define_sample_order, fit_nonlinear, log_transform_df, log_transform_dm, long_to_matrix, matrix_to_long, merge_rare_levels, normalize_data_df, normalize_data_dm, normalize_sample_medians_df, normalize_sample_medians_dm, plot_CV_distr, plot_CV_distr.df, plot_PCA, plot_PVCA, plot_PVCA.df, plot_boxplot, plot_corr_matrix, plot_heatmap_diagnostic, plot_heatmap_generic, plot_hierarchical_clustering, plot_iRT, plot_peptide_corr_distribution, plot_peptide_corr_distribution.corrDF, plot_peptides_of_one_protein, plot_protein_corrplot, plot_sample_corr_distribution, plot_sample_corr_distribution.corrDF, plot_sample_corr_heatmap, plot_sample_mean, plot_single_feature, plot_spike_in, plot_split_violin_with_boxplot, plot_with_fitting_curve, prepare_PVCA_df, quantile_normalize_df, quantile_normalize_dm, sample_annotation_to_colors, unlog_df, unlog_dm Package: PROcess Exports: bslnoff, isPeak, pk2bmkr, getMzs, lnn, quality, sigma, getPeaks, noise, read.files, specZoom, intg, peaks, rmBaseline, renorm, binning, gelmap, aveSpec, align, getPeaks2, avesd, is.multiple Package: procoil Exports: readCCModel, writeCCModel ExportMethods: predict, show, plot, weights, profile, fitted, heatmap ExportClasses: CCModel, CCProfile Package: proFIA Exports: acquisitionDirectory, analyzeAcquisitionFIA, dataMatrix, determiningInjectionZone, determiningSizePeak.Geom, estimateNoiseMS, findBandsFIA, findFIASignal, getInjectionPeak, groupMatrix, injectionPeaks, phenoClasses, plotNoise, proFIAset ExportMethods: plotSamplePeaks, plotRaw, plotFlowgrams, plot, phenoClasses, peaksGroup, peaks, makeDataMatrix, injectionPeaks, impute.randomForest, impute.KNN_TN, impute.FIA, groupMatrix, group.FIA, findMzGroup, exportVariableMetadata, exportSampleMetadata, exportPeakTable, exportExpressionSet, exportDataMatrix, dataMatrix ExportClasses: proFIAset Package: profileplyr Exports: BamBigwig_to_chipProfile, annotateRanges, as_profileplyr, clusterRanges, convertToEnrichedHeatmapMat, export_deepToolsMat, generateEnrichedHeatmap, groupBy, import_deepToolsMat, orderBy, params, sampleData, summarize ExportMethods: summarize, sampleData, orderBy, groupBy, export_deepToolsMat, convertToEnrichedHeatmapMat, clusterRanges, c, annotateRanges_great, annotateRanges, sampleData<- ExportClasses: profileplyr Package: profileScoreDist Exports: ProfileDist, backgroundDist, computeScoreDist, plotDist, regularizeMatrix, scoreDistCutoffs, signalDist Package: progeny Exports: progeny Package: projectR Exports: auc_mat, cluster2pattern, clusterPlotR, correlateR, geneMatchR, intersectoR, projectR, rotatoR ExportClasses: rotatoR, correlateR Package: pRoloc Exports: markerMSnSet, unknownMSnSet, sampleMSnSet, testMSnSet, getPredictions, getMarkers, getMarkerClasses, minClassScore, testMarkers, minMarkers, addMarkers, pRolocmarkers, empPvalues, getStockcol, getStockpch, setStockcol, setStockpch, getLisacol, setLisacol, getOldcol, setOldcol, getUnknowncol, getUnknownpch, setUnknowncol, setUnknownpch, zerosInBinMSnSet, filterBinMSnSet, filterZeroCols, filterZeroRows, fDataToUnknown, plot2D, plot2Dmethods, plotEllipse, plot2Ds, data1, data2, col1, col2, move2Ds, addLegend, plotDist, mrkHClust, mrkConsProfiles, highlightOnPlot, highlightOnPlot3D, SpatProtVis, orgQuants, checkFvarOverlap, checkFeatureNamesOverlap, classWeights, plsdaRegularisation, plsdaOptimisation, plsdaOptimization, plsdaPrediction, plsdaClassification, svmRegularisation, svmOptimisation, svmOptimization, svmPrediction, svmClassification, ksvmRegularisation, ksvmOptimisation, ksvmOptimization, ksvmPrediction, ksvmClassification, knnRegularisation, knnOptimisation, knnOptimization, knnPrediction, knnClassification, nbRegularisation, nbOptimisation, nbOptimization, nbPrediction, nbClassification, nnetRegularisation, nnetOptimisation, nnetOptimization, nnetPrediction, nnetClassification, perTurboOptimisation, perTurboOptimization, perTurboClassification, getParams, getRegularisedParams, getRegularizedParams, rfRegularisation, rfOptimisation, rfOptimization, rfPrediction, rfClassification, phenoDisco, tagmMapTrain, tagmPredict, tagmMapPredict, tagmMcmcPredict, tagmMcmcTrain, tagmMcmcProcess, mcmc_get_outliers, mcmc_burn_chains, mcmc_get_meanComponent, mcmc_get_meanoutliersProb, mcmc_thin_chains, mcmc_pool_chains, logPosteriors, chains, geweke_test, favourPrimary, combineThetaRegRes, knntlOptimisation, knntlClassification, thetas, lopims, lopims1, lopims2, lopims3, lopims4, lopims5, goIdToTerm, goTermToId, flipGoTermId, prettyGoTermId, showGOEvidenceCodes, getGOEvidenceCodes, setAnnotationParams, getAnnotationParams, getGOFromFeatures, makeGoSet, mrkVecToMat, mrkMatToVec, mrkMatAndVec, showMrkMat, isMrkMat, isMrkVec, addGoAnnotations, filterMinMarkers, filterMaxMarkers, subsetMarkers, orderGoAnnotations, clustDist, ClustDistList, getNormDist, QSep, qsep, plotConsProfiles ExportMethods: chi2, show, MLearn, getWarnings, getSeed, getF1Scores, f1Count, levelPlot, plot, plot3D, nndist ExportClasses: GenRegRes, ThetaRegRes, MAPParams, AnnotationParams, SpatProtVis, ClustDist, ClustDistList, QSep Package: pRolocGUI Exports: pRolocVis Package: PROMISE Exports: PROMISE, avg.abs.genestat, jung.rstat, spearman.rstat, promise.genestat Package: PROPER Exports: RNAseq.SimOptions.2grp, simRNAseq, runSims, comparePower, summaryPower, power.seqDepth, plotPower, plotPowerTD, plotPowerFD, plotFDR, plotFDcost, plotPowerAlpha, plotPowerHist, plotAll, estParam Package: Prostar Exports: Prostar Package: proteinProfiles Exports: filterFeatures, grepAnnotation, profileDistance, plotProfileDistance Package: ProteomicsAnnotationHubData Exports: ProteomicsAnnotationHubData, makeAnnotationHubMetadata, writePahdTemplate, readPahdFiles, PAHD, availableProteomicsAnnotationHubData, proteomicsAnnotationHubDataResources, identicalRemLoc ExportClasses: PAHD Package: ProteoMM Exports: MBimpute, convert_log2, eig_norm1, eig_norm2, eigen_pi, g.test, get_presAbs_prots, makeLMFormula, make_intencities, make_meta, peptideLevel_DE, peptideLevel_PresAbsDE, plot_3_pep_trends_NOfile, plot_volcano, plot_volcano_wLab, prot_level_multiMat_PresAbs, prot_level_multi_part, subset_proteins Package: PSEA Exports: marker, crplot, em_quantvg, swlm, fmm, lmfitst, slt, pvalmat, coefmat Package: psichomics Exports: assignValuePerPatient, assignValuePerSubject, calculateLoadingsContribution, convertGeneIdentifiers, correlateGEandAS, createGroupByAttribute, createGroupByColumn, diffAnalyses, ensemblToUniprot, filterGeneExpr, filterGroups, filterPSI, getAttributesTime, getColumnsTime, getDownloadsFolder, getFirebrowseCohorts, getFirebrowseDataTypes, getFirebrowseDates, getGeneList, getGenesFromSplicingEvents, getGtexTissues, getMatchingSamples, getPSIperPatient, getPatientFromSample, getSampleFromPatient, getSampleFromSubject, getSplicingEventFromGenes, getSplicingEventTypes, getSubjectFromSample, getValuePerPatient, getValuePerSubject, groupPerElem, groupPerPatient, groupPerSample, isFirebrowseUp, labelBasedOnCutoff, listSplicingAnnotations, loadAnnotation, loadFirebrowseData, loadGtexData, loadLocalFiles, loadSRAproject, normaliseGeneExpression, optimalPSIcutoff, optimalSurvivalCutoff, parseCategoricalGroups, parseMatsAnnotation, parseMisoAnnotation, parseSampleGroups, parseSplicingEvent, parseSuppaAnnotation, parseTcgaSampleInfo, parseVastToolsAnnotation, performICA, performPCA, plotCorrelation, plotDistribution, plotGeneExprPerSample, plotGroupIndependence, plotICA, plotPCA, plotProtein, plotRowStats, plotSurvivalCurves, plotSurvivalPvaluesByCutoff, plotTranscripts, plotVariance, prepareAnnotationFromEvents, prepareGeneQuant, prepareJunctionQuant, prepareSRAmetadata, processSurvTerms, psichomics, quantifySplicing, queryEnsemblByEvent, queryEnsemblByGene, readFile, rowMeans, rowVars, survdiffTerms, testGroupIndependence, testSurvival ExportMethods: colSums Package: PSICQUIC Exports: PSICQUIC, IDMapper, interactionTypes, detectionMethods, speciesIDs ExportMethods: interactions, providers, rawQuery, addGeneInfo, addStandardNames, show ExportClasses: PSICQUIC, IDMapper Package: psygenet2r Exports: enrichedPD, extractSentences, geneAttrPlot, getUMLs, jaccardEstimation, ndisease, ngene, pantherGraphic, plot, psygenetDisease, psygenetDiseaseSentences, psygenetGene, psygenetGeneSentences, topAnatEnrichment ExportMethods: extract ExportClasses: JaccardIndexPsy, DataGeNET.Psy Package: pulsedSilac Exports: assayNamesPept<-, assayNamesProt<-, assaysPept<-, assaysProt<-, linkerDf<-, metaoptions<-, rowDataPept<-, rowDataProt<-, rownamesPept<-, rownamesProt<-, PeptExp, ProtExp, SilacPeptideExperiment, SilacProteinExperiment, SilacProteomicsExperiment, addMisscleavedPeptides, assayNamesPept, assayNamesProt, assaysPept, assaysProt, barplotCounts, barplotTimeCoverage, buildLinkerDf, calculateAIC, calculateIsotopeFraction, calculateIsotopeRatio, calculateOldIsotopePool, compareAIC, filterByMissingTimepoints, linkerDf, mergeModelsLists, metaoptions, modelTurnover, mostStable, plotDistributionAssay, plotDistributionModel, plotIndividualModel, rowDataPept, rowDataProt, rownamesPept, rownamesProt, scatterCompareAssays, scatterCompareModels, subsetPept, subsetProt, upsetTimeCoverage ExportMethods: upsetTimeCoverage, subsetProt, subsetPept, subset, scatterCompareAssays, rownamesProt, rownamesPept, rowDataProt, rowDataPept, rowData, rbind, plotIndividualModel, plotDistributionAssay, nrow, ncol, mostStable, modelTurnover, metaoptions, metadata, merge, linkerDf, length, filterByMissingTimepoints, dim, colnames, colData, coerce, cbind, calculateOldIsotopePool, calculateIsotopeRatio, calculateIsotopeFraction, barplotTimeCoverage, barplotCounts, assaysProt, assaysPept, assays, assayNamesProt, assayNamesPept, assayNames, addMisscleavedPeptides, rownamesProt<-, rownamesPept<-, rowDataProt<-, rowDataPept<-, rowData<-, metaoptions<-, metadata<-, linkerDf<-, colnames<-, colData<-, assaysProt<-, assaysPept<-, assays<-, assayNamesProt<-, assayNamesPept<-, [, $<-, $ ExportClasses: SilacProteomicsExperiment, SilacProteinExperiment, SilacPeptideExperiment Package: PureCN Exports: annotateTargets, bootstrapResults, calculateBamCoverageByInterval, calculateGCContentByInterval, calculateIntervalWeights, calculateLogRatio, calculateMappingBiasVcf, calculatePowerDetectSomatic, calculateTangentNormal, callAlterations, callAlterationsFromSegmentation, callAmplificationsInLowPurity, callCIN, callLOH, callMutationBurden, correctCoverageBias, createCurationFile, createNormalDatabase, createTargetWeights, filterIntervals, filterTargets, filterVcfBasic, filterVcfMuTect, filterVcfMuTect2, findFocal, getSexFromCoverage, getSexFromVcf, plotAbs, poolCoverage, predictSomatic, preprocessIntervals, processMultipleSamples, readCoverageFile, readCurationFile, readLogRatioFile, readSegmentationFile, runAbsoluteCN, segmentationCBS, segmentationHclust, segmentationPSCBS, setMappingBiasVcf, setPriorVcf Package: Pviz Exports: ATrack, CladeTrack, DTrack, ProbeTrack, ProteinAxisTrack, ProteinSequenceTrack, plot_clade, plot_inter ExportClasses: ProteinSequenceTrack, ProteinAxisTrack, ProbeTrack, DTrack, CladeTrack, ATrack Package: PWMEnrich Exports: getBackgroundFrequencies, makeBackground, makePriors, makePWMCutoffBackground, makePWMEmpiricalBackground, makePWMGEVBackground, makePWMLognBackground, makePWMPvalCutoffBackground, makePWMPvalCutoffBackgroundFromSeq, motifDiffEnrichment, motifEcdf, motifEnrichment, motifIC, motifScores, motifSimilarity, PFMtoPWM, plotMotifScores, plotMultipleMotifs, PWMUnscaled, readMotifs, registerCoresPWMEnrich, scanWithPWM, seqLogoGrid, useBigMemoryPWMEnrich, toPWM ExportMethods: sequenceReport, reverseComplement, plotTopMotifsSequence, plotTopMotifsGroup, plot, motifRankingForSequence, motifRankingForGroup, groupReport, as.data.frame ExportClasses: PWMLognBackground, PWMGEVBackground, PWMEmpiricalBackground, PWMCutoffBackground, PWM, MotifEnrichmentResults, MotifEnrichmentReport Package: pwOmics Exports: readOmics, readTFdata, readPWdata, identifyPWs, identifyTFs, identifyPWTFTGs, identifyRsofTFs, getOmicsTimepoints, getOmicsallGeneIDs, getOmicsallProteinIDs, getOmicsDataset, getDS_PWs, getDS_TFs, getDS_TGs, getUS_TFs, getUS_PWs, getUS_regulators, getBiopaxModel, getProteinIntersection, getTFIntersection, getGenesIntersection, gettpIntersection, staticConsensusNet, consDynamicNet, clusterTimeProfiles, plotConsensusGraph, plotConsDynNet, plotConsensusProfiles, plotTimeProfileClusters, findSignalingAxes, get_matching_transcripts, generate_DSSignalingBase, readPhosphodata, identifyPR, infoConsensusGraph, temp_correlations Package: pwrEWAS Exports: pwrEWAS, pwrEWAS_deltaDensity, pwrEWAS_powerPlot, pwrEWAS_shiny Package: qckitfastq Exports: GC_content, adapter_content, calc_adapter_content, calc_format_score, calc_over_rep_seq, dimensions, find_format, gc_per_read, kmer_count, overrep_kmer, overrep_reads, per_base_quality, per_read_quality, plot_GC_content, plot_adapter_content, plot_overrep_kmer, plot_overrep_reads, plot_per_base_quality, plot_per_read_quality, plot_read_content, plot_read_length, qual_score_per_read, read_base_content, read_content, read_length, run_all Package: qcmetrics Exports: QcMetric, QcMetrics, QcMetadata, qcshow, as.data.frame.QcMetrics, Qc2Tex, Qc2Tex2, Qc2Tex3, Qc2Rmd, rnadeg, n15qc ExportMethods: status, status<-, name, name<-, qcdata, qcdata<-, qcenv, qcenv<-, metadata, metadata<-, mdata, mdata<-, names, names<-, description, description<-, show, plot, print, show<-, plot<-, [, [[, qcReport ExportClasses: QcMetric, QcMetrics, QcMetadata Package: QDNAseq Exports: addPhenodata, applyFilters, binReadCounts, callBins, compareToReference, correctBins, estimateCorrection, exportBins, frequencyPlot, getBinAnnotations, highlightFilters, isobarPlot, makeCgh, noisePlot, normalizeBins, normalizeSegmentedBins, plot, poolRuns, segmentBins, smoothOutlierBins, createBins, calculateMappability, calculateBlacklist, calculateBlacklistByRegions, iterateResiduals, chromosomes, bpstart, bpend ExportClasses: QDNAseqReadCounts, QDNAseqCopyNumbers Package: qpcrNorm Exports: calcCV, ctQc, matrixByPlate, normQpcrHouseKeepingGenes, normQpcrQuantile, normQpcrRankInvariant, plotVarMean, readQpcr, readQpcrBatch, writeQpcr ExportClasses: qpcrBatch Package: qpgraph Exports: qpHist, qpGraphDensity, qpCliqueNumber, qpClique, qpBoundary, qpAnyGraph, qpGetCliques, qpUpdateCliquesRemoving, qpIPF, qpHTF, qpPAC, qpPCC, qpRndGraph, qpRndWishart, qpG2Sigma, qpUnifRndAssociation, qpK2ParCor, qpPrecisionRecall, qpPRscoreThreshold, qpImportNrr, qpTopPairs, qpPlotNetwork, qpPlotMap, qpCov, erGraphParam, dRegularGraphParam, erMarkedGraphParam, dRegularMarkedGraphParam, eQTLcrossParam, eQTLnetworkEstimationParam, filterCollinearities ExportMethods: qpNrr, qpAvgNrr, qpGenNrr, qpGraph, qpPAC, qpPCC, qpCItest, qpAllCItests, qpEdgeNrr, qpEdgeCor, qpPathWeight, qpFunctionalCoherence, show, det, determinant, dim, dimnames, summary, rmvnorm, rcmvnorm, sim.cross, plot, rgraphBAM, UGgmm, HMgmm, rUGgmm, rHMgmm, $, eQTLcross, reQTLcross, addGenes, addeQTL, addGeneAssociation, alleQTL, ciseQTL, transeQTL, allGeneAssociations, geneticMap, physicalMap, graph, ggData, markerNames, geneNames, geneAnnotation, eQTLnetworkEstimate, varExplained, resetCutoffs ExportClasses: SsdMatrix, erGraphParam, dRegularGraphParam, erMarkedGraphParam, dRegularMarkedGraphParam, UGgmm, HMgmm, eQTLcross, eQTLcrossParam, eQTLnetworkEstimationParam, eQTLnetwork, qpGraph Package: qPLEXanalyzer Exports: assignColours, computeDiffStats, convertToMSnset, corrPlot, coveragePlot, getContrastResults, groupScaling, hierarchicalPlot, intensityBoxplot, intensityPlot, maVolPlot, normalizeQuantiles, normalizeScaling, pcaPlot, peptideIntensityPlot, plotMeanVar, regressIntensity, rliPlot, rowScaling, summarizeIntensities, mergePeptides Package: qrqc Exports: readSeqFile, makeReport, getBase, getKmer, getBaseProp, getQual, getGC, getMCQual, getSeqlen, basePlot, qualPlot, seqlenPlot, gcPlot, geom_qlinerange, list2df, scale_color_iupac, scale_color_dna, kmerKLPlot, kmerEntropyPlot, calcKL, plotQuals, plotBases, plotSeqLengths, plotGC Package: qsea Exports: addCNV, addCoverage, addSeqPref, addPatternDensity, addOffset, addLibraryFactors, addEnrichmentParameters, makeTable, isSignificant, getPCA, plotCNV, plotCoverage, plotEnrichmentProfile, plotEPmatrix, regionStats, createQseaSet, normMethod, addContrast, fitNBglm, getExampleQseaSet, addNewSamples ExportMethods: getSampleTable, getSampleNames, getSampleGroups, getChrNames, getParameters, getRegions, getWindowSize, getLibSize, getOffset, getCNV, hasCNV, getCounts, getZygosity, setZygosity, plotPCA, plotPCAfactors ExportClasses: qseaSet, qseaGLM, qseaPCA Package: qsmooth Exports: qsmooth, qsmoothPlotWeights, qstats ExportMethods: qsmoothWeights, qsmoothData ExportClasses: qsmooth Package: QSutils Exports: Collapse, ConsSeq, CorrectGapsAndNs, DBrule, Diverge, DNA.dist, DottedAlignment, DSFT, FAD, fn.ab, FreqMat, GenerateVars, geom.series, GetInfProfile, GetQSData, GetRandomSeq, GiniSimpson, HCq, Hill, IntersectStrandHpls, MutationFreq, MutsTbl, NucleotideDiversity, PolyDist, Rao, ReadAmplSeqs, Recollapse, Renyi, ReportVariants, SegSites, Shannon, SortByMutations, SummaryMuts, TotalMutations, UniqueMutations Package: Qtlizer Exports: get_qtls Package: quantro Exports: MSbetween, MSwithin, anova, matboxplot, matdensity, quantro, quantroPlot, quantroPvalPerm, quantroStat, quantroStatPerm, summary ExportMethods: summary, quantroStatPerm, quantroStat, quantroPvalPerm, anova, MSwithin, MSbetween ExportClasses: quantro Package: quantsmooth Exports: quantsmooth, quantsmooth.seg, quantsmooth.cv, getLambdaMin, plotSmoothed, getChangedRegions, getChangedIdx, numericCHR, characterCHR, scaleto, plotChromosome, prepareGenomePlot, paintCytobands, lengthChromosome, drawSimpleChrom, position2Cytoband, grid.chromosome Package: QuartPAC Exports: getMutations, makeAlignedSuperStructure, quartCluster Package: QuasR Exports: qAlign, qCount, preprocessReads, qExportWig, qQCReport, qMeth, alignmentStats, qProfile, qProjectUpdate ExportMethods: length, genome, auxiliaries, alignments, [, show ExportClasses: qProject Package: QuaternaryProd Exports: QP_Pmf, QP_Probability, QP_Pvalue, QP_SigPvalue, QP_Support, RunCRE_HSAStringDB Package: qusage Exports: qusage, qgen, makeComparison, aggregateGeneSet, calcVIF, oneWay.pVal, pdf.pVal, twoWay.pVal, twoCurve.pVal, getXcoords, calcBayesCI, newQSarray, qsTable, numFeatures, numPathways, plotGeneSetDistributions, plotDensityCurves, plotCIs, plotCIsGenes, read.gmt, combinePDFs, plotCombinedPDF ExportMethods: plot, print, dim, head, summary, [<- ExportClasses: QSarray Package: qvalue Exports: empPvals, lfdr, pi0est, qvalue, write.qvalue Package: R3CPET Exports: ChiapetExperimentData, NetworkCollection, HLDAResult, ChromMaintainers ExportMethods: loadPETs, pet, tfbs, loadTFBS, loadPPI, ppi, pet<-, tfbs<-, ppi<-, createIndexes, PrepareData, CreateCenteredBED, buildNetworks, networks, sizes, TF, InferNetworks, clusterInteractions, getClusters, getRegionsIncluster, getRegionsInNetwork, topEdges, topNodes, wordsPerTopic, docPerTopic, betas, updateResults, outputGenesPerClusterToDir, outputGenesPerNetworkToDir, GOEnrich.folder, GOEnrich.networks, GenerateNetworks, annotateExpression, plot3CPETRes, visualizeCircos, visualizeInteractions, plotTrack, createServer ExportClasses: cluesOrSota, ChiapetExperimentData, NetworkCollection, HLDAResult, ChromMaintainers Package: r3Cseq Exports: getCoverage, expCoverage, contrCoverage, getRawReads, expRawData, expRawData<-, contrRawData, contrRawData<-, getBatchRawReads, getReadCountPerRestrictionFragment, getBatchReadCountPerRestrictionFragment, getReadCountPerWindow, getBatchReadCountPerWindow, getViewpoint, calculateRPM, calculateBatchRPM, expReadCount, contrReadCount, expRPM, contrRPM, getInteractions, getBatchInteractions, expInteractionRegions, contrInteractionRegions, plotOverviewInteractions, plotInteractionsNearViewpoint, plotInteractionsPerChromosome, plotDomainogramNearViewpoint, plot3Cecdf, export3CseqRawReads2bedGraph, export3Cseq2bedGraph, exportInteractions2text, exportBatchInteractions2text, generate3CseqReport, getExpInteractionsInRefseq, getContrInteractionsInRefseq ExportClasses: r3Cseq, r3CseqInBatch Package: R453Plus1Toolbox Exports: extendedCIGARToList, listToExtendedCIGAR, readSFF, writeSFF, qualityReportSFF ExportMethods: alignShortReads, readsOnTarget, coverageOnTarget, calculateTiTv, genomeSequencerMIDs, sequenceCaptureLinkers, demultiplexReads, removeLinker, filterChimericReads, detectBreakpoints, mergeBreakpoints, annotateVariants, annotatedVariants, htmlReport, ava2vcf, plotVariationFrequency, plotAmpliconCoverage, plotVariants, plotChimericReads, seqsC1, seqsC1<-, seqsC2, seqsC2<-, commonBpsC1, commonBpsC1<-, commonBpsC2, commonBpsC2<-, commonAlignC1, commonAlignC1<-, commonAlignC2, commonAlignC2<-, alignedReadsC1, alignedReadsC1<-, alignedReadsC2, alignedReadsC2<-, MapperSet, AVASet, fDataAmp, featureDataAmp, featureDataAmp<-, assayDataAmp, assayDataAmp<-, getAlignedReads, referenceSequences, referenceSequences<-, getReadStatus, getVariantPercentages, setVariantFilter, name, name<-, flowgramFormat, flowgramFormat<-, flowChars, flowChars<-, keySequence, keySequence<-, clipQualityLeft, clipQualityLeft<-, clipQualityRight, clipQualityRight<-, clipAdapterLeft, clipAdapterLeft<-, clipAdapterRight, clipAdapterRight<-, flowgram, flowgram<-, flowgrams, flowgrams<-, flowIndexes, flowIndexes<-, read, read<-, quality, quality<-, reads, reads<-, addRead, getRead, sff2fastq, readLengthStats, readLengthHist, baseQualityStats, baseQualityHist, sequenceQualityHist, positionQualityBoxplot, baseFrequency, nucleotideCharts, gcContent, gcPerPosition, gcContentHist, complexity.dust, complexity.entropy, dinucleotideOddsRatio, flowgramBarplot, homopolymerHist ExportClasses: AVASet, MapperSet, AnnotatedVariants, Breakpoints, SFFRead, SFFContainer Package: R4RNA Exports: as.helix, is.helix, blankPlot, maxHeight, collapseHelix, expandHelix, defaultPalette, colourByValue, colourByCount, colourByConservation, colourByCovariation, colourByCanonical, colourByBasepairFrequency, colourByUnknottedGroups, unknottedGroups, basepairFrequency, alignmentPercentGaps, alignmentConservation, alignmentCovariation, alignmentCanonical, helixCovariation, helixConservation, helixCanonical, basepairCovariation, basepairConservation, basepairCanonical, baseConservation, isConflictingHelix, isDuplicatingHelix, isOverlappingHelix, plotCovariance, plotDoubleCovariance, plotOverlapCovariance, plotArc, plotArcs, plotHelix, plotDoubleHelix, plotOverlapHelix, readConnect, readHelix, readVienna, readBpseq, viennaToHelix, helixToVienna, helixToBpseq, helixToConnect, writeHelix, logseq, logceiling, logfloor, structureMismatchScore Package: RaggedExperiment Exports: RaggedExperiment, compactAssay, compactSummarizedExperiment, disjoinAssay, disjoinSummarizedExperiment, qreduceAssay, qreduceSummarizedExperiment, sparseAssay, sparseSummarizedExperiment ExportMethods: subsetByOverlaps, show, seqinfo, rowRanges, rowData, overlapsAny, mcols, length, dimnames, dim, colData, assays, assayNames, assay, seqinfo<-, rowRanges<-, rowData<-, mcols<-, dimnames<-, colData<-, [ ExportClasses: RaggedExperiment Package: rain Exports: rain Package: rama Exports: arrange.row, est.shift, fit.model, is.row.na, ls.effect, mat.mean, ratio.plot, weight.plot Package: ramwas Exports: ramwasParameters, ramwasAnnotateLocations, isAbsolutePath, makefullpath, cachedRDSload, findBestNpvs, pvalue2qvalue, orthonormalizeCovariates, parameterDump, parameterPreprocess, parametersFromFile, ramwas0createArtificialData, ramwas1scanBams, pipelineProcessBam, ramwas2collectqc, ramwas3normalizedCoverage, ramwas4PCA, ramwas5MWAS, ramwas6annotateTopFindings, ramwas7ArunMWASes, ramwas7BrunElasticNet, ramwas7CplotByNCpGs, ramwas7riskScoreCV, processCommandLine, qcmean, qqPlotFast, qqPlotPrepare, manPlotPrepare, manPlotFast, plotPCvalues, plotPCvectors, plotROC, plotPrediction, plotCVcors, rowSumsSq, colSumsSq, testPhenotype, getCpGsetALL, getCpGsetCG, getLocations, getMWAS, getMWASandLocations, getMWASrange, getDataByLocation, subsetCoverageDirByLocation, madeBED, madeBEDrange, madeBEDgraph, madeBEDgraphRange, insilicoFASTQ, injectSNPsMAF, mat2cols, estimateFragmentSizeDistribution, plotFragmentSizeDistributionEstimate, ramwasSNPs ExportClasses: rwDataClass Package: RandomWalkRestartMH Exports: Random.Walk.Restart.Multiplex, Random.Walk.Restart.MultiplexHet, compute.adjacency.matrix, compute.transition.matrix, create.multiplex, create.multiplexHet, create.multiplexHetNetwork.topResults, create.multiplexNetwork.topResults, isMultiplex, isMultiplexHet, isRWRMH_Results, isRWRM_Results, normalize.multiplex.adjacency Package: randPack Exports: getTreatment, getEnrolleeInfo, createTrial, validPID, makeRandomizer, treatmentFactors, factorNames, treatmentNames, numberOfTreatments, treatmentFactors, numberOfFactorLevels, minimizeTaves, minimizePocSim, simPats ExportMethods: randomization<- ExportClasses: ClinicalExperiment, ClinicalTrial, PatientData, PatientID, Randomizer, RandomizerDesc Package: RankProd Exports: topGene, RP, RPadvance, RSadvance, RankProducts, plotRP, RP.advance Package: Rariant Exports: acCi, nhsCi, scoreTest, nmTest, feTest, ciOutside, ciCovers, ciOverlap, ciWidth, plotConfidenceIntervals, plotAbundanceShift, coverageProbability, ciAdjustLevel, rariant, rariantStandalone, pos2gr, gr2pos, readRariant, writeRariant, rariantInspect, splitSampleBinom, tallyBamRegion, eventFillScale, verdictColorScale, rateFillScale, baseFillScale, yesNoMaybe, updateCalls, mergeCalls, filterCalls, findCalls, evidenceHeatmap, tallyPlot Package: RBGL Exports: articulationPoints, astarSearch, aver.wavefront, bandwidth, bellman.ford.sp, betweenness.centrality.clustering, biConnComp, boyerMyrvoldPlanarityTest, brandes.betweenness.centrality, chrobakPayneStraightLineDrawing, circle.layout, circleLayout, clusteringCoef, clusteringCoefAppr, connectedComp, cuthill.mckee.ordering, dag.sp, dijkstra.sp, dominatorTree, edgeConnectivity, edmondsOptimumBranching, edmondsMaxCardinalityMatching, edmonds.karp.max.flow, extractPath, floyd.warshall.all.pairs.sp, fruchtermanReingoldForceDirectedLayout, gprofile, graphGenerator, gursoyAtunLayout, highlyConnSG, incremental.components, init.incremental.components, isKuratowskiSubgraph, isomorphism, isStraightLineDrawing, is.triangulated, ith.wavefront, johnson.all.pairs.sp, kamada.kawai.spring.layout, kamadaKawaiSpringLayout, kCliques, kCores, kingOrdering, kolmogorov.max.flow, lambdaSets, lengauerTarjanDominatorTree, makeBiconnectedPlanar, makeConnected, makeMaximalPlanar, maxClique, maximumCycleRatio, maxWavefront, minCut, minDegreeOrdering, minimumCycleRatio, mstree.kruskal, mstree.prim, planarCanonicalOrdering, planarFaceTraversal, prim.minST, push.relabel.max.flow, randomGraphLayout, removeSelfLoops, rms.wavefront, same.component, separates, sequential.vertex.coloring, sloan.ordering, sloanStartEndVertices, sp.between, sp.between.scalar, strongComp, transitive.closure, transitivity, tsort ExportMethods: bfs, dfs Package: RBioinf Exports: simpleSort, simpleRand, asSimpleVector, Rcal, subClassNames, superClassNames, simplePVect, LPO, superClasses, class2Graph, S4Help, computeClassLinearization, randDNA, subsetAsCharacter, setVNames, convertMode, printWithNumbers, classList2Graph, traceMethods Package: rBiopaxParser Exports: CLASS_INHERITANCE_BP2, CLASS_INHERITANCE_BP3, CLASS_PROPERTIES_BP2, CLASS_PROPERTIES_BP3, DATABASE_BIOPAX, addBiochemicalReaction, addBiopaxInstance, addBiopaxInstances, addControl, addPathway, addPathwayComponents, addPhysicalEntity, addPhysicalEntityParticipant, addPropertiesToBiopaxInstance, calcGraphOverlap, colorGraphNodes, combineNodes, createBiopax, diffGraphs, downloadBiopaxData, generateNewUniqueID, getClassProperties, getInstanceClass, getInstanceProperty, getNeighborhood, getReferencedIDs, getReferencingIDs, getSubClasses, getSuperClasses, getXrefAnnotations, hasProperty, intersectGraphs, isOfClass, layoutRegulatoryGraph, listComplexComponents, listInstances, listInteractionComponents, listPathwayComponents, listPathways, mergePathways, pathway2AdjacancyMatrix, pathway2Geneset, pathway2Graph, pathway2RegulatoryGraph, plotRegulatoryGraph, readBiopax, removeInstance, removeNodes, removeProperties, selectInstances, splitComplex, transitiveClosure, transitiveReduction, uniteGraphs, writeBiopax Package: RBM Exports: RBM_T, RBM_F Package: Rbowtie2 Exports: adapterremoval_usage, adapterremoval_version, bowtie2, bowtie2_build, bowtie2_build_usage, bowtie2_usage, bowtie2_version, identify_adapters, remove_adapters Package: rbsurv Exports: rbsurv, rbsurv.default Package: Rcade Exports: RcadeAnalysis, defineBins, countReads, diffCountsBaySeq, constructRcadeTable ExportMethods: plotMM, plotBB, plotBBB, plotPCA, exportRcade, getDE, getChIP, getRcade, getDE<-, getChIP<-, getRcade<- ExportClasses: Rcade, RcadeTrack Package: RCAS Exports: calculateCoverageProfile, calculateCoverageProfileFromTxdb, calculateCoverageProfileList, calculateCoverageProfileListFromTxdb, createControlRegions, createDB, createOrthologousGeneSetList, deleteSampleDataFromDB, discoverFeatureSpecificMotifs, extractSequences, getFeatureBoundaryCoverage, getFeatureBoundaryCoverageBin, getFeatureBoundaryCoverageMulti, getIntervalOverlapMatrix, getMotifSummaryTable, getTargetedGenesTable, getTxdbFeatures, getTxdbFeaturesFromGRanges, importBed, importBedFiles, importGtf, parseMsigdb, plotFeatureBoundaryCoverage, printMsigdbDataset, queryGff, retrieveOrthologs, runGSEA, runMotifRG, runReport, runReportMetaAnalysis, runTopGO, summarizeDatabaseContent, summarizeQueryRegions, summarizeQueryRegionsMulti Package: rcellminer Exports: DrugData, MolData, compareFingerprints, crossCors, getAct, getActivityRangeStats, getAllFeatureData, getBinaryMutationData, getColumnQuantiles, getDrugActivityData, getDrugActivityRange, getDrugActivityRepeatData, getDrugMoaList, getDrugName, getESetList, getFeatureAnnot, getFeatureDataFromMatList, getFingerprintList, getMedSenLineActivity, getMinDrugActivityRepeatCor, getMoaStr, getMoaToCompounds, getMolDataMatrices, getMolDataType, getNumDrugActivityRepeats, getNumMissingLines, getRepeatAct, getRsd, getSampleData, getSmiles, hasMoa, isPublic, loadCellminerPlotInfo, loadNciColorSet, parCorPatternComparison, passRuleOf5, passRuleOf5FromNsc, patternComparison, plotCellMiner, plotCellMiner2D, plotDrugActivityRepeats, plotDrugSets, plotStructures, plotStructuresFromNscs, rcdkplot, removeMolDataType, restrictFeatureMat, rowCors, runShinyApp, runShinyComparePlots, runShinyCompareStructures, runShinyCompoundBrowser, searchForNscs, selectCorrelatedRows, selectCorrelatedRowsFromMatrices ExportMethods: initialize, getSampleData, getRepeatAct, getFeatureAnnot, getESetList, getAllFeatureData, getAct, MolData, DrugData, [[<-, [[ ExportClasses: MolData, DrugData Package: RchyOptimyx Exports: RchyOptimyx, summary, plot, merge Package: RcisTarget Exports: addLogo, addMotifAnnotation, addSignificantGenes, aucScores, calcAUC, cisTarget, getColumnNames, getMotifAnnotation, getRowNames, getSignificantGenes, importAnnotations, importRankings, rankingRcisTarget, reRank ExportMethods: show, rownames, nrow, ncol, getRanking, getNumColsInDB, getMaxRank, getAUC, colnames ExportClasses: rankingRcisTarget Package: RCM Exports: RCM, RCM_NB, addOrthProjection, extractCoord, inertia, liks, plotRespFun, residualPlot ExportMethods: RCM Package: Rcpi Exports: acc, calcDrugFPSim, calcDrugMCSSim, calcParProtGOSim, calcParProtSeqSim, calcTwoProtGOSim, calcTwoProtSeqSim, checkProt, convMolFormat, extractDrugAIO, extractDrugALOGP, extractDrugAminoAcidCount, extractDrugApol, extractDrugAromaticAtomsCount, extractDrugAromaticBondsCount, extractDrugAtomCount, extractDrugAutocorrelationCharge, extractDrugAutocorrelationMass, extractDrugAutocorrelationPolarizability, extractDrugBCUT, extractDrugBPol, extractDrugBondCount, extractDrugCPSA, extractDrugCarbonTypes, extractDrugChiChain, extractDrugChiCluster, extractDrugChiPath, extractDrugChiPathCluster, extractDrugDescOB, extractDrugECI, extractDrugEstate, extractDrugEstateComplete, extractDrugExtended, extractDrugExtendedComplete, extractDrugFMF, extractDrugFragmentComplexity, extractDrugGraph, extractDrugGraphComplete, extractDrugGravitationalIndex, extractDrugHBondAcceptorCount, extractDrugHBondDonorCount, extractDrugHybridization, extractDrugHybridizationComplete, extractDrugHybridizationRatio, extractDrugIPMolecularLearning, extractDrugKR, extractDrugKRComplete, extractDrugKappaShapeIndices, extractDrugKierHallSmarts, extractDrugLargestChain, extractDrugLargestPiSystem, extractDrugLengthOverBreadth, extractDrugLongestAliphaticChain, extractDrugMACCS, extractDrugMACCSComplete, extractDrugMDE, extractDrugMannholdLogP, extractDrugMomentOfInertia, extractDrugOBFP2, extractDrugOBFP3, extractDrugOBFP4, extractDrugOBMACCS, extractDrugPetitjeanNumber, extractDrugPetitjeanShapeIndex, extractDrugPubChem, extractDrugPubChemComplete, extractDrugRotatableBondsCount, extractDrugRuleOfFive, extractDrugShortestPath, extractDrugShortestPathComplete, extractDrugStandard, extractDrugStandardComplete, extractDrugTPSA, extractDrugVABC, extractDrugVAdjMa, extractDrugWHIM, extractDrugWeight, extractDrugWeightedPath, extractDrugWienerNumbers, extractDrugXLogP, extractDrugZagrebIndex, extractPCMBLOSUM, extractPCMDescScales, extractPCMFAScales, extractPCMMDSScales, extractPCMPropScales, extractPCMScales, extractProtAAC, extractProtAPAAC, extractProtCTDC, extractProtCTDD, extractProtCTDT, extractProtCTriad, extractProtDC, extractProtGeary, extractProtMoran, extractProtMoreauBroto, extractProtPAAC, extractProtPSSM, extractProtPSSMAcc, extractProtPSSMFeature, extractProtQSO, extractProtSOCN, extractProtTC, getCPI, getDrug, getFASTAFromKEGG, getFASTAFromUniProt, getMolFromCAS, getMolFromChEMBL, getMolFromDrugBank, getMolFromKEGG, getMolFromPubChem, getPDBFromRCSBPDB, getPPI, getProt, getSeqFromKEGG, getSeqFromRCSBPDB, getSeqFromUniProt, getSmiFromChEMBL, getSmiFromDrugBank, getSmiFromKEGG, getSmiFromPubChem, readFASTA, readMolFromSDF, readMolFromSmi, readPDB, searchDrug, segProt Package: Rcwl Exports: arguments<-, baseCommand<-, cwlClass<-, cwlVersion<-, extensions<-, hints<-, requirements<-, stdOut<-, steps<-, InputArrayParam, InputParam, InputParamList, OutputArrayParam, OutputParam, OutputParamList, Step, arguments, baseCommand, cwlClass, cwlParam, cwlShiny, cwlStepParam, cwlVersion, extensions, hints, inputs, outputs, plotCWL, readCWL, requirements, runCWL, runCWLBatch, runs, short, stdOut, stepInParam, stepInParamList, stepParam, stepParamList, steps, writeCWL ExportMethods: +, $<-, $ ExportClasses: stepParamList, stepParam, stepInParamList, stepInParam, cwlStepParam, cwlParam, OutputParamList, OutputParam, OutputArrayParam, InputParamList, InputParam, InputArrayParam Package: RcwlPipelines Exports: AnnPhaseVcf, BaseRecal, BedToIntervalList, CalculateContamination, ColSeqArtifact, CombineVariants, DepthOfCoverage, FilterMutectCalls, FilterOBias, Funcotator, GAlign, GPoN, GenomicsDB, GetPileupSummaries, LoFreq, MuSE, Mutect2, Mutect2PL, PoN, RSeQC, ReadBackedPhasing, RenameSampleInVcf, STAR, SamToFastq, SomaticCallers, SomaticSniper, SortVcf, VarDict, VarScan2Somatic, VarScan2_processSomatic, VarScan2_somatic, VarScan2_somaticFilter, alignMerge, annovar, bam_readcount, bcfview, bgzip, blastn, bowtie2, bowtie2_build, bowtie_build, bwa, bwaAlign, bwaMMRecal, bwaMRecal, bwa_index, cnvkit_batch, cutadapt, cwlTools, fastqc, featureCounts, geneBody_coverage, genePredToBed, gtfToGenePred, hapCall, hisat2_align, hisat2_build, htseq, jdCall, kallisto_index, kallisto_quant, lancet, makeblastdb, manta, mantaStrelka, markdup, mergeBam, mergeBamDup, miRDeep2, miRDeep2PL, miRMapper, multiqc, mvOut, neusomatic, phaseVcf, polysolver, pvacseq, read_distribution, rnaseq_Sf, runWDL, salmon_index, salmon_quant, sam2bam, samtools_flagstat, samtools_index, samtools_mpileup, sortBam, starFusion, strelka, tabix_index, vcfCoverage, vcfExpression, vcf_expression_annotator, vcf_readcount_annotator, vep, vt_decompose Package: RCy3 Exports: AddToGroup, RemoveFromGroup, addCyEdges, addCyNodes, applyFilter, bundleEdges, clearEdgeBends, clearEdgePropertyBypass, clearNetworkCenterBypass, clearNetworkPropertyBypass, clearNetworkZoomBypass, clearNodeOpacityBypass, clearNodePropertyBypass, clearSelection, cloneNetwork, closeSession, collapseGroup, commandEcho, commandOpenDialog, commandPause, commandQuit, commandRunFile, commandSleep, commandsAPI, commandsGET, commandsHelp, commandsPOST, commandsRun, copyVisualStyle, createColumnFilter, createCompositeFilter, createDegreeFilter, createGraphFromNetwork, createGroup, createGroupByColumn, createIgraphFromNetwork, createNetworkFromDataFrames, createNetworkFromGraph, createNetworkFromIgraph, createSubnetwork, createVisualStyle, cybrowserClose, cybrowserDialog, cybrowserHide, cybrowserList, cybrowserSend, cybrowserShow, cybrowserVersion, cyrestAPI, cyrestDELETE, cyrestGET, cyrestPOST, cyrestPUT, cytoscapeApiVersions, cytoscapeFreeMemory, cytoscapeMemoryStatus, cytoscapeNumberOfCores, cytoscapePing, cytoscapeVersionInfo, deleteAllNetworks, deleteDuplicateEdges, deleteGroup, deleteNetwork, deleteSelectedEdges, deleteSelectedNodes, deleteSelfLoops, deleteStyleMapping, deleteTableColumn, deleteVisualStyle, diffusionAdvanced, diffusionBasic, disableApp, dockPanel, enableApp, expandGroup, exportFilters, exportImage, exportNetwork, exportNetworkToNDEx, exportVisualStyles, fitContent, floatPanel, getAllEdges, getAllNodes, getAppInformation, getAppStatus, getAppUpdates, getArrowShapes, getAvailableApps, getBackgroundColorDefault, getCollectionList, getCollectionName, getCollectionNetworks, getCollectionSuid, getDisabledApps, getEdgeColor, getEdgeCount, getEdgeInfo, getEdgeLineStyle, getEdgeLineWidth, getEdgeProperty, getEdgeSelectionColorDefault, getEdgeTargetArrowShape, getFilterList, getFirstNeighbors, getGroupInfo, getInstalledApps, getLayoutNameMapping, getLayoutNames, getLayoutPropertyNames, getLayoutPropertyType, getLayoutPropertyValue, getLineStyles, getNetworkCenter, getNetworkCount, getNetworkList, getNetworkNDExId, getNetworkName, getNetworkProperty, getNetworkSuid, getNetworkViewSuid, getNetworkViews, getNetworkZoom, getNodeColor, getNodeCount, getNodeHeight, getNodePosition, getNodeProperty, getNodeSelectionColorDefault, getNodeShapes, getNodeSize, getNodeWidth, getSelectedEdgeCount, getSelectedEdges, getSelectedNodeCount, getSelectedNodes, getStyleDependencies, getTableColumnNames, getTableColumnTypes, getTableColumns, getTableValue, getUninstalledApps, getVisualPropertyDefault, getVisualPropertyNames, getVisualStyleNames, hideAllPanels, hideEdges, hideNodes, hidePanel, hideSelectedEdges, hideSelectedNodes, importFilters, importNetworkFromFile, importNetworkFromNDEx, importVisualStyles, installApp, invertEdgeSelection, invertNodeSelection, layoutCopycat, layoutNetwork, listGroups, loadTableData, lockNodeDimensions, makeSimpleGraph, makeSimpleIgraph, mapTableColumn, mapVisualProperty, matchArrowColorToEdge, openAppStore, openSession, removeNodeCustomGraphics, renameNetwork, renameTableColumn, saveSession, selectAllEdges, selectAllNodes, selectEdges, selectEdgesAdjacentToSelectedNodes, selectEdgesConnectingSelectedNodes, selectFirstNeighbors, selectNodes, selectNodesConnectedBySelectedEdges, setBackgroundColorDefault, setCurrentNetwork, setCurrentView, setEdgeColorBypass, setEdgeColorDefault, setEdgeColorMapping, setEdgeFontFaceBypass, setEdgeFontFaceDefault, setEdgeFontFaceMapping, setEdgeFontSizeBypass, setEdgeFontSizeDefault, setEdgeFontSizeMapping, setEdgeLabelBypass, setEdgeLabelColorBypass, setEdgeLabelColorDefault, setEdgeLabelColorMapping, setEdgeLabelDefault, setEdgeLabelMapping, setEdgeLabelOpacityBypass, setEdgeLabelOpacityDefault, setEdgeLabelOpacityMapping, setEdgeLineStyleBypass, setEdgeLineStyleDefault, setEdgeLineStyleMapping, setEdgeLineWidthBypass, setEdgeLineWidthDefault, setEdgeLineWidthMapping, setEdgeOpacityBypass, setEdgeOpacityDefault, setEdgeOpacityMapping, setEdgePropertyBypass, setEdgeSelectionColorDefault, setEdgeSourceArrowColorBypass, setEdgeSourceArrowColorDefault, setEdgeSourceArrowColorMapping, setEdgeSourceArrowMapping, setEdgeSourceArrowShapeBypass, setEdgeSourceArrowShapeDefault, setEdgeSourceArrowShapeMapping, setEdgeTargetArrowColorBypass, setEdgeTargetArrowColorDefault, setEdgeTargetArrowColorMapping, setEdgeTargetArrowMapping, setEdgeTargetArrowShapeBypass, setEdgeTargetArrowShapeDefault, setEdgeTargetArrowShapeMapping, setEdgeTooltipBypass, setEdgeTooltipDefault, setEdgeTooltipMapping, setLayoutProperties, setNetworkCenterBypass, setNetworkPropertyBypass, setNetworkZoomBypass, setNodeBorderColorBypass, setNodeBorderColorDefault, setNodeBorderColorMapping, setNodeBorderOpacityBypass, setNodeBorderOpacityDefault, setNodeBorderOpacityMapping, setNodeBorderWidthBypass, setNodeBorderWidthDefault, setNodeBorderWidthMapping, setNodeColorBypass, setNodeColorDefault, setNodeColorMapping, setNodeComboOpacityMapping, setNodeCustomBarChart, setNodeCustomBoxChart, setNodeCustomHeatMapChart, setNodeCustomLineChart, setNodeCustomLinearGradient, setNodeCustomPieChart, setNodeCustomPosition, setNodeCustomRadialGradient, setNodeCustomRingChart, setNodeFillOpacityBypass, setNodeFillOpacityDefault, setNodeFillOpacityMapping, setNodeFontFaceBypass, setNodeFontFaceDefault, setNodeFontFaceMapping, setNodeFontSizeBypass, setNodeFontSizeDefault, setNodeFontSizeMapping, setNodeHeightBypass, setNodeHeightDefault, setNodeHeightMapping, setNodeLabelBypass, setNodeLabelColorBypass, setNodeLabelColorDefault, setNodeLabelColorMapping, setNodeLabelDefault, setNodeLabelMapping, setNodeLabelOpacityBypass, setNodeLabelOpacityDefault, setNodeLabelOpacityMapping, setNodeOpacityBypass, setNodePropertyBypass, setNodeSelectionColorDefault, setNodeShapeBypass, setNodeShapeDefault, setNodeShapeMapping, setNodeSizeBypass, setNodeSizeDefault, setNodeSizeMapping, setNodeTooltipBypass, setNodeTooltipDefault, setNodeTooltipMapping, setNodeWidthBypass, setNodeWidthDefault, setNodeWidthMapping, setStyleDependencies, setVisualPropertyDefault, setVisualStyle, syncNodeCustomGraphicsSize, toggleGraphicsDetails, unhideAll, unhideEdges, unhideNodes, uninstallApp, updateApp, updateNetworkInNDEx, updateStyleDefaults, updateStyleMapping Package: RCyjs Exports: RCyjs, createTestGraph, eda, edaNames, noa, noaNames, simpleDemoGraph ExportMethods: vAlign, showNodes, showEdges, showAll, sfn, setZoom, setPosition, setNodeWidth, setNodeSizeRule, setNodeSize, setNodeShape, setNodeLabelRule, setNodeLabelAlignment, setNodeHeight, setNodeFontSize, setNodeFontColor, setNodeColorRule, setNodeColor, setNodeBorderWidth, setNodeBorderColor, setNodeAttributes, setGraph, setEdgeStyle, setEdgeAttributes, setDefaultStyle, setDefaultNodeWidth, setDefaultNodeSize, setDefaultNodeShape, setDefaultNodeHeight, setDefaultNodeFontSize, setDefaultNodeFontColor, setDefaultNodeColor, setDefaultNodeBorderWidth, setDefaultNodeBorderColor, setDefaultEdgeWidth, setDefaultEdgeTargetArrowShape, setDefaultEdgeTargetArrowColor, setDefaultEdgeSourceArrowShape, setDefaultEdgeSourceArrowColor, setDefaultEdgeLineStyle, setDefaultEdgeLineColor, setDefaultEdgeColor, setBackgroundColor, selectNodes, selectFirstNeighborsOfSelectedNodes, savePNG, saveLayout, saveJPG, restoreLayout, redraw, loadStyleFile, layoutSelectionInGridInferAnchor, layoutSelectionInGrid, layout, invertNodeSelection, hideSelectedNodes, hideNodes, hideEdges, hideAllEdges, hAlign, getZoom, getSupportedNodeShapes, getSupportedEdgeDecoratorShapes, getSelectedNodes, getPosition, getNodes, getNodeCount, getLayoutStrategies, getJSON, getEdgeCount, fitSelection, fit, deleteSelectedNodes, deleteGraph, clearSelection, addGraphFromFile, addGraph ExportClasses: RCyjs Package: RDAVIDWebService Exports: as ExportMethods: upsideDown, universeMappedCount, universeCounts, uniqueIds, type, terms, summary, subset, species, show, setTimeOut, setHttpProtocolVersion, setEmail, setCurrentSpecies, setCurrentGeneListPosition, setCurrentBackgroundPosition, setAnnotationCategories, popTotals, popHits, plot2D, percentages, membership, members, listTotals, is.connected, initialize, ids, getTimeOut, getStub, getSpecieNames, getListName, getIdTypes, getHttpProtocolVersion, getGeneListReportFile, getGeneListReport, getGeneListNames, getGeneCategoriesReport, getFunctionalAnnotationTableFile, getFunctionalAnnotationTable, getFunctionalAnnotationChartFile, getFunctionalAnnotationChart, getEmail, getDefaultCategoryNames, getCurrentSpeciesPosition, getCurrentGeneListPosition, getCurrentBackgroundListPosition, getClusterReportFile, getClusterReport, getBackgroundListNames, getAnnotationSummary, getAllAnnotationCategoryNames, genes, foldEnrichments, fdrs, enrichment, duplicateIds, dictionary, counts, connect, cluster, categories, bonferronis, benjaminis, addList, DAVIDTermCluster, DAVIDGenes, DAVIDGeneCluster, DAVIDGODag, DAVIDFunctionalAnnotationTable, DAVIDFunctionalAnnotationChart ExportClasses: DAVIDTermCluster, DAVIDResult, DAVIDGenes, DAVIDGeneCluster, DAVIDGODag, DAVIDFunctionalAnnotationTable, DAVIDFunctionalAnnotationChart, DAVIDCluster Package: rDGIdb Exports: queryDGIdb, sourceDatabases, interactionTypes, geneCategories, resultSummary, searchTermSummary, byGene, detailedResults, resourceVersions, plotInteractionsBySource Package: Rdisop Exports: addMolecules, decomposeIsotopes, decomposeMass, getMass, getFormula, getIsotope, getValid, getMolecule, getScore, initializeCHNOPS, initializeCHNOPSMgKCaFe, initializeCHNOPSNaK, initializeElements, initializePSE, initializeCharges, isotopeScore, subMolecules Package: RDRToolbox Exports: Isomap, LLE, generateData, plotDR, SwissRoll, DBIndex Package: ReactomeGSA Exports: ReactomeAnalysisRequest, add_dataset, get_reactome_analysis_result, get_reactome_analysis_status, get_reactome_data_types, get_reactome_methods, get_result, open_reactome, pathways, perform_reactome_analysis, plot_correlations, plot_volcano, reactome_links, remove_dataset, result_types, set_method, set_parameters ExportMethods: show, print, names ExportClasses: ReactomeAnalysisResult Package: ReactomePA Exports: cnetplot, dotplot, emapplot, enrichPathway, geneID, geneInCategory, gsePathway, gseaplot, heatplot, ridgeplot, viewPathway Package: ReadqPCR Exports: read.taqman, read.qPCR, checkValidTaqmanFilenames, checkValidqPCRFilename, exprs.well.order, exprs.well.order<-, read.LC480, read.LC480SampleInfo, qpcR2CyclesSet, effs, effs<-, se.effs, se.effs<- ExportMethods: merge ExportClasses: qPCRBatch, CyclesSet Package: REBET Exports: rebet Package: recount Exports: abstract_search, add_metadata, add_predictions, all_metadata, browse_study, coverage_matrix, download_retry, download_study, expressed_regions, find_geo, geo_characteristics, geo_info, getRPKM, getTPM, read_counts, reproduce_ranges, scale_counts, snaptron_query Package: recoup Exports: buildAnnotationStore, calcCoverage, coverageRef, coverageRnaRef, getAnnotation, getBiotypes, getr, kmeansDesign, mergeRuns, preprocessRanges, profileMatrix, recoup, recoupCorrelation, recoupHeatmap, recoupProfile, recoupPlot, removeData, setr, sliceObj Package: RedeR Exports: RedPort, gtoy.rm, att.setv, att.sete, att.mapv, att.mape, subg, cea, .rederpost ExportMethods: calld, ping, version, updateGraph, getGraph, addGraph, addSeries, duplicateGraph, addSubgraph, addSubgraph.list, addLegend.color, addLegend.size, addLegend.shape, relax, getNodes, getNodeIDs, addNodes, deleteNodes, nestNodes, nesthc, updateContainerSize, mergeOutEdges, getContainerComponets, mergeNodes, getEdges, getEdgeIDs, getSourceEdgeIDs, getTargetEdgeIDs, setArrowDirection, addEdges, deleteEdges, addEdgeBetweenContainers, selectEdges, selectNodes, selectAllEdges, selectAllNodes, selectGraph, deSelectEdges, deSelectNodes, deSelectGraph, deleteSelectedEdges, deleteSelectedNodes, isDynamicsActive, exitd, resetd ExportClasses: RedPort Package: REDseq Exports: buildREmap, assignSeq2REsite, binom.test.REDseq, compareREDseq, distanceHistSeq2RE, summarizeByRE, plotCutDistribution, summarizeBySeq Package: RefNet Exports: RefNet, pubmedAbstract, detectDuplicateInteractions, pickBestFromDupGroup ExportMethods: interactions, providerClasses, providers, show ExportClasses: RefNet Package: RefPlus Exports: colMedians, normalize.quantiles2, rma.para, rmaplus, rmaref.predict Package: regioneR Exports: characterToBSGenome, circularRandomizeRegions, commonRegions, createFunctionsList, createRandomRegions, emptyCacheRegioneR, extendRegions, filterChromosomes, getChromosomesByOrganism, getGenome, getGenomeAndMask, getMask, joinRegions, listChrTypes, localZScore, maskFromBSGenome, meanDistance, meanInRegions, mergeRegions, numOverlaps, overlapGraphicalSummary, overlapPermTest, overlapRegions, permTest, plotRegions, print.permTestResults, randomizeRegions, recomputePermTest, resampleRegions, splitRegions, subtractRegions, toDataframe, toGRanges, uniqueRegions Package: regionReport Exports: DESeq2Report, derfinderReport, edgeReport, renderReport, templateDensity, templateHistogram, templateManhattan, templatePvalueDensity, templatePvalueHistogram Package: regsplice Exports: LRTests, LR_stats, RegspliceData, RegspliceResults, countsData, createDesignMatrix, df_tests, filterLowCounts, filterZeros, fitFullMultiple, fitNullMultiple, fitRegMultiple, gene_IDs, initializeResults, p_adj, p_vals, regsplice, runNormalization, runVoom, summaryTable, weightsData ExportMethods: weightsData, rowData, p_vals, p_adj, gene_IDs, df_tests, countsData, colData, assays, LR_stats, [ ExportClasses: RegspliceResults, RegspliceData Package: REMP Exports: GRannot, fetchRMSK, fetchRefSeqGene, findRECpG, getBackend, getGM12878, grooMethy, initREMP, remp, rempTemplate, remp_options, remp_reset, remprofile ExportMethods: saveParcel, remplot, rempTrim, rempStats, rempQC, rempM, rempImp, rempCombine, rempB, rempAnnot, rempAggregate, getRefGene, getRECpG, getRE, getParcelInfo, getILMN, details, decodeAnnot ExportClasses: REMProduct, REMParcel Package: Repitools ExportMethods: show ExportClasses: FastQC, SequenceQC, SequenceQCSet, ScoresList, ClusteredScoresList, QdnaData, BayMethList Package: ReportingTools Exports: HTMLReport, CSVFile, DataPackage, validConnection, reporting.theme.alternate, reporting.theme, makeDESeqDF, readReport, fileHandlers, connectionHandlers, knitrHandlers, shinyHandlers, fileWIndexHandlers, makeOldHTMLReport, custHeaderPanel ExportMethods: publish, name, title, title<-, reportDirectory, reportDirectory<-, filename, path, url, page, page<-, finish, show, basePath, baseUrl, dependencies, dependencies<-, modifyReportDF, objectToHTML, toReportDF, Link ExportClasses: DataPackage, CSVFile, HTMLReport, BaseReport, HTMLReportRef, ReportHandlers Package: RepViz Exports: RepViz Package: ReQON Exports: ReQON, ReadPosErrorPlot, QualFreqPlot, FWSEplot Package: restfulSE Exports: BQ3_Array, BQ3_Source, BQM_Array, BQM_Source, RESTfulSummarizedExperiment, basic_clinvars, bqConn, cgcConn, goPatt, gtexTiss, isbCgcDatasets, isbCgcTables, pancan_SE, se1.3M, se100k, seByTumor, tasicCortex ExportMethods: dimnames, dim, assays, assayNames, assay, RESTfulSummarizedExperiment, [ ExportClasses: RESTfulSummarizedExperiment, BQSummarizedExperiment, BQM_Source, BQM_Matrix, BQM_Array, BQ3_Source, BQ3_Matrix, BQ3_Array Package: rexposome Exports: classification, clustering, correlation, expos, exposureNames, extract, exwas, familyNames, highAndLow, ilod, imputation, imputeLOD, loadExposome, loadImputed, mexwas, ndim, normalityTest, pca, phenotypeNames, plot3PCA, plotClassification, plotCorrelation, plotEXP, plotEffect, plotExwas, plotFamily, plotHistogram, plotLOD, plotMissings, plotPCA, plotPHE, plotVolcano, readExposome, standardize, tableLOD, tableMissings, tef, toES, trans, volcano_plot ExportClasses: mExWAS, imExposomeSet, ExposomeSet, ExposomePCA, ExposomeCorr, ExposomeClust, ExWAS Package: rfPred ExportMethods: rfPred_scores Package: rGADEM Exports: GADEM, readPWMfile ExportMethods: dim, names, consensus, parameters, startPos, endPos, nOccurrences, nMotifs, plot, getPWM ExportClasses: parameters, align, gadem, motif Package: RGalaxy Exports: galaxy, functionToGalaxify, anotherTestFunction, GalaxyConfig, GalaxyOutput, getFriendlyName, GalaxyInputFile, testFunctionWithSelect, testFunctionWithGalaxySelectParam, RserveConnection, GalaxyIntegerParam, GalaxyNumericParam, GalaxyCharacterParam, GalaxyLogicalParam, GalaxySelectParam, gstop, gwarning, gmessage, runFunctionalTest, probeLookup, addTwoNumbers, addTwoNumbersWithTest ExportClasses: GalaxyIntegerParam, GalaxyNumericParam, GalaxyCharacterParam, GalaxyLogicalParam, GalaxySelectParam, RserveConnection, GalaxyConfig, GalaxyOutput, GalaxyInputFile Package: RGMQL Exports: ALL, ANY, ASC, AVG, BAG, BAGD, COUNT, COUNTSAMP, DESC, DG, DGE, DL, DLE, DOWN, MAX, MD, MEDIAN, META, MIN, NIL, Q1, Q2, Q3, SQRT, STD, SUM, UP, compile_query, compile_query_fromfile, conds, delete_dataset, download_as_GRangesList, download_dataset, execute, export_gmql, filter_and_extract, import_gmql, init_gmql, login_gmql, logout_gmql, read_GRangesList, read_gmql, register_gmql, remote_processing, run_query, run_query_fromfile, sample_metadata, sample_region, save_query, save_query_fromfile, semijoin, show_datasets_list, show_job_log, show_jobs_list, show_queries_list, show_samples_list, show_schema, stop_gmql, stop_job, trace_job, upload_dataset ExportMethods: union, take, setdiff, select, merge, map, group_by, filter, extend, cover, collect, arrange, aggregate Package: RGraph2js Exports: getDefaultOptions, getEdgesDataFrame, getNodesDataFrame, graph2js, graph2json Package: Rgraphviz Exports: agopen, agopenSimple, agread, agwrite, buildEdgeList, buildNodeList, checkAttrs, drawAgNode, drawTxtLabel, getDefaultAttrs, getNodeLabels, getNodeNames, graphvizVersion, graphvizCapabilities, graphLayout, makeNodeAttrs, pieGlyph, removedEdges, toFile, layoutGraph ExportMethods: graphDataDefaults, graphDataDefaults<-, graphData, graphData<-, clusterData, clusterData<-, nodeDataDefaults, nodeDataDefaults<-, nodeData, nodeData<-, edgeDataDefaults, edgeDataDefaults<-, edgeData, edgeData<-, AgEdge<-, AgEdge, AgNode<-, AgNode, agraph, arrowhead, arrowsize, arrowtail, bezierPoints, bLines, botLeft, boundBox, color, cPoints, edgemode, edgeNames, ep, fillcolor, from, getNodeCenter, getNodeHeight, getNodeLW, getNodeRW, getNodeXY, getPoints, getSpline, getX, getY, head, labelColor, labelFontsize, labelJust, labelLoc, labelText, labelWidth, laidout, layoutType, lines, name, numSplines, plot, pointList, shape, show, sp, splines, style, tail, to, toDot, txtLabel, upRight, renderGraph ExportClasses: AgEdge, AgNode, AgTextLabel, BezierCurve, boundingBox, pEdge, pNode, Ragraph, xyPoint Package: rGREAT Exports: GreatJob, submitGreatJob, GreatJob ExportMethods: plotRegionGeneAssociationGraphs, getEnrichmentTables, availableOntologies, availableCategories ExportClasses: GreatJob Package: RGSEA Exports: RGSEAsd, RGSEApredict, RGSEAfix Package: rgsepd Exports: GSEPD_INIT, GSEPD_PCA_Plot, GSEPD_PCA_Spec, GSEPD_Process, GSEPD_ProcessAll, GSEPD_DEGHeatmap, GSEPD_ChangeConditions, GSEPD_ChangeOutput, GSEPD_PullDEG, GSEPD_Heatmap, Name_to_RefSeq, DisplayName, GSEPD_Export_DESeq, ExtractProjection Package: rhdf5 Exports: H5open, H5close, H5garbage_collect, H5get_libversion, H5Acreate, H5Aopen, H5Aopen_by_name, H5Aopen_by_idx, H5Aexists, H5Aclose, H5Adelete, H5Aget_name, H5Aget_space, H5Aget_type, H5Aread, H5Awrite, H5Dclose, H5Dcreate, H5Dget_type, H5Dget_create_plist, H5Dget_space, H5Dopen, H5Dread, H5Dwrite, H5Dget_storage_size, H5Dset_extent, H5Fclose, H5Fcreate, H5Fflush, H5Fopen, H5Fis_hdf5, H5Fget_filesize, H5Fget_name, H5Fget_create_plist, H5Fget_access_plist, H5Gclose, H5Gcreate, H5Gcreate_anon, H5Gget_info, H5Gget_info_by_idx, H5Gget_info_by_name, H5Gopen, H5Iget_name, H5Iget_type, H5Iis_valid, H5Lcreate_external, H5Lexists, H5Lget_info, H5Ldelete, H5Lmove, H5Lcopy, H5Oopen, H5Oclose, H5Oget_num_attrs, H5Oget_num_attrs_by_name, H5Sclose, H5Scopy, H5Screate, H5Screate_simple, H5Sget_simple_extent_dims, H5Sset_extent_simple, H5Sis_simple, H5Sselect_index, H5Sselect_hyperslab, H5Sunlimited, H5Tcopy, H5Tset_size, H5Pcreate, H5Pget_class, H5Pcopy, H5Pclose, H5Pclose_class, H5Pset_libver_bounds, H5Pget_libver_bounds, H5Pset_char_encoding, H5Pget_char_encoding, H5Pset_create_intermediate_group, H5Pget_create_intermediate_group, H5Pset_layout, H5Pget_layout, H5Pset_chunk, H5Pget_chunk, H5Pset_deflate, H5Pset_fill_value, H5Pfill_value_defined, H5Pset_fill_time, H5Pget_fill_time, H5Pset_alloc_time, H5Pget_alloc_time, H5Pall_filters_avail, H5Pget_nfilters, H5Pset_chunk_cache, H5Pequal, h5const, h5constType, h5createDataset, h5createFile, h5createGroup, h5createAttribute, h5default, h5dump, h5ls, h5read, h5readAttributes, h5save, h5write, h5write.default, h5writeDataset, h5writeDataset.data.frame, h5writeDataset.list, h5writeDataset.matrix, h5writeDataset.integer, h5writeDataset.double, h5writeDataset.logical, h5writeDataset.character, h5writeDataset.array, h5writeAttribute, h5writeAttribute.matrix, h5writeAttribute.integer, h5writeAttribute.double, h5writeAttribute.logical, h5writeAttribute.character, h5writeAttribute.array, h5delete, h5listIdentifier, h5validObjects, h5version, h5set_extent, h5errorHandling, h5closeAll, h5testFileLocking, h5disableFileLocking, h5enableFileLocking ExportClasses: H5IdComponent Package: rhdf5client Exports: transfermode<-, H5S_Array, H5S_dataset2, H5S_source, HSDSArray, HSDSDataset, HSDSFile, HSDSSource, HSDS_Matrix, HSDS_Matrix_OLD, URL_h5serv, URL_hsds, dataset, domains, dsmeta, fetchDatasets, getData, getDatasetAttrs, getDatasetSlice, getDatasetUUIDs, getDims, getHRDF, getReq, groups, hsdsInfo, internalDim, isplit, links, listDatasets, listDomains, setPath, sproc, targets ExportMethods: setPath, links, hsdsInfo, groups, domains, dimnames, dim, [[, [ ExportClasses: HSDSMatrix, HSDSArray, H5S_source, H5S_dataset, H5S_Matrix, H5S_Array Package: Rhdf5lib Exports: getHdf5Version, pkgconfig Package: Rhisat2 Exports: extract_splice_sites, hisat2, hisat2_build, hisat2_build_usage, hisat2_usage, hisat2_version Package: Rhtslib Exports: pkgconfig Package: RiboProfiling Exports: aroundPromoter, codonInfo, codonPCA, countShiftReads, countsPlot, histMatchLength, orfRelativePos, plotSummarizedCov, printPCA, readStartCov, readsToStartOrEnd, riboSeqFromBAM Package: riboSeqR Exports: readRibodata, findCDS, frameCounting, readingFrame, filterHits, plotCDS, plotTranscript, sliceCounts, rnaCounts, plotFS, lengthDist, libScales, logoContext ExportMethods: dim, [, show Package: RImmPort Exports: Events, Findings, Interventions, SpecialPurpose, Study, TrialDesign, buildNewSqliteDb, getAssayDataOfStudies, getDomainCode, getDomainDataOfStudies, getListOfAssayTypes, getListOfDomains, getListOfStudies, getStudiesWithSpecificAssayData, getStudiesWithSpecificDomainData, getStudy, loadSerializedStudyData, mergeDomainAndSupplemental, serialzeStudyData, setImmPortDataSource ExportClasses: TrialDesign, Study, SpecialPurpose, Interventions, Findings, Events Package: Ringo Exports: autocor, chipAlongChrom1, corPlot, image, image.RGList, computeRunningMedians, sliding.quantile, findChersOnSmoothed, cherByThreshold, newCher, relateChers, preprocess, nimblegenScale, readNimblegen, asExprSet, as.data.frame.cherList, ftr2xys, compute.gc, posToProbeAnno, validProbeAnno, regionOverlap, features2Probes, sliding.meansd, computeSlidingT, getFeats, upperBoundNull, extractProbeAnno, exportCherList, plotBM, twoGaussiansNull, chipAlongChrom, quantilesOverPositions, sigGOTable, chersToBED ExportMethods: get, ls, initialize, plot, show, arrayName, chromosomeNames, genome, probes, arrayName<-, genome<-, update, cellType, cellType<-, nonzero, cbind2 ExportClasses: probeAnno, cher, qop Package: Risa Exports: readISAtab, updateAssayMetadata, write.ISAtab, write.investigation.file, write.assay.file, write.study.file, getAnnotatedDataFrameAssay, getStudyFilename, getRawDataFilenames, getRawDataFilenames, getAssayRawDataFilenames, processAssayXcmsSet, processAssayXcmsSet.1factor, getMSAssayFilenames, isMSAssay, getMicroarrayAssayFilenames, isMicroarrayAssay, getMIAMEMetadata, getExpressionSet, suggestBiocPackage ExportClasses: ISATab Package: RITAN Exports: as.graph, check_any_net_input, check_net_input, enrichment_symbols, geneset_overlap, icon_test, load_geneset_symbols, network_overlap, readGMT, readSIF, resource_reduce, show_active_genesets_hist, term_enrichment, term_enrichment_by_subset, writeGMT, write_simple_table Package: RIVER Exports: appRIVER, evaRIVER, getData, getFuncRvFeat, getFuncRvPosteriors, integratedEM, mleBeta, mleTheta, plotPosteriors, testPosteriors Package: RJMCMCNucleosomes Exports: mergeAllRDSFilesFromDirectory, mergeRDSFiles, plotNucleosomes, postTreatment, rjmcmc, rjmcmcCHR, segmentation Package: RLMM Exports: Classify, create_Thetafile, normalize_Rawfiles, plot_theta Package: Rmagpie Exports: plotErrorsRepeatedOneLayerCV, plotErrorsSummaryOneLayerCV, plotErrorsFoldTwoLayerCV ExportMethods: initialize, runOneLayerExtCV, runTwoLayerExtCV, show, getResults, getDataset, getDataset<-, getNoFolds1stLayer, getNoFolds1stLayer<-, getNoFolds2ndLayer, getNoFolds2ndLayer<-, getClassifierName, getClassifierName<-, getSvmKernel, getSvmKernel<-, getNoOfRepeats, getNoOfRepeats<-, getTypeFoldCreation, getTypeFoldCreation<-, getFeatureSelectionOptions, getFeatureSelectionOptions<-, getMaxSubsetSize, getMaxSubsetSize<-, getSubsetsSizes, getOptionValues, getOptionValues<-, getSubsetsSizes<-, getSpeed, getSpeed<-, getNoModels, getGenesFromBestToWorst, getModels, getNoThresholds, getNoThresholds<-, getFinalClassifier, rankedGenesImg, getResult1LayerCV, getResult2LayerCV, findFinalClassifier, classifyNewSamples ExportClasses: geneSubsets, assessment, finalClassifier, thresholds Package: rmelting Exports: melting, meltingBatch Package: RmiR ExportClasses: miRtcList Package: Rmmquant Exports: RmmquantClassExample, RmmquantExample, RmmquantRun, counts ExportMethods: show, counts Package: RNAdecay Exports: a_high, a_low, aic, aicc, b_low, cols, comb_cv, const_decay, constraint_fun_list_maker, decay_plot, decaying_decay, fit_var, group_map, groupings, log_lik, mod_optimization, n_par, plain_theme, sse_null_const_decay, sse_null_decaying_decay 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: RNAmodR Exports: settings<-, CoverageSequenceData, CoverageSequenceDataFrame, End3SequenceData, End3SequenceDataFrame, End5SequenceData, End5SequenceDataFrame, EndSequenceData, EndSequenceDataFrame, ModDNASequenceTrack, ModInosine, ModRNASequenceTrack, ModSetInosine, Modifier, ModifierSet, NormEnd3SequenceData, NormEnd3SequenceDataFrame, NormEnd5SequenceData, NormEnd5SequenceDataFrame, PileupSequenceData, PileupSequenceDataFrame, ProtectedEndSequenceData, ProtectedEndSequenceDataFrame, RNASequenceTrack, SequenceData, SequenceDataList, SequenceDataSet, aggregate, aggregateData, bamfiles, compare, compareByCoord, dataType, findMod, getAggregateData, getData, getDataTrack, hasAggregateData, labelByCoord, mainScore, modType, modifications, modifierType, modify, pileupToCoverage, plotCompare, plotCompareByCoord, plotData, plotDataByCoord, plotROC, replicates, sequenceData, sequences, settings, subsetByCoord, validAggregate, validModification ExportMethods: validModification, validAggregate, subsetByCoord, settings, sequences, sequenceData, seqtype, seqinfo, replicates, rbind, ranges, plotROC, plotDataByCoord, plotData, plotCompareByCoord, pileupToCoverage, names, modify, modifierType, modifications, modType, mainScore, labelByCoord, hasAggregateData, getDataTrack, getData, getAggregateData, findMod, dataType, conditions, compareByCoord, cbind, bamfiles, aggregateData, aggregate, SequenceData, ModifierSet, Modifier, settings<-, seqtype<-, [ ExportClasses: SequenceDataSet, SequenceDataList, SequenceDataFrame, SequenceDFrame, RNASequenceTrack, RNAModifier, ProtectedEndSequenceDataFrame, ProtectedEndSequenceData, PileupSequenceDataFrame, PileupSequenceData, NormEnd5SequenceDataFrame, NormEnd5SequenceData, NormEnd3SequenceDataFrame, NormEnd3SequenceData, ModifierSet, Modifier, ModSetInosine, ModRNASequenceTrack, ModInosine, ModDNASequenceTrack, EndSequenceDataFrame, EndSequenceData, End5SequenceDataFrame, End5SequenceData, End3SequenceDataFrame, End3SequenceData, DNAModifier, CoverageSequenceDataFrame, CoverageSequenceData Package: RNAmodR.AlkAnilineSeq Exports: ModAlkAnilineSeq, ModSetAlkAnilineSeq ExportMethods: plotDataByCoord, plotData, getDataTrack, findMod, aggregateData, settings<- ExportClasses: ModSetAlkAnilineSeq, ModAlkAnilineSeq Package: RNAmodR.ML Exports: setMLModel<-, aggregate_example, find_mod_example, getMLModel, hasMLModel, trainingData, useMLModel, useModel ExportMethods: useModel, useMLModel, trainingData, modify, hasMLModel, getMLModel, aggregate, setMLModel<- ExportClasses: RNAModifierML, ModifierMLranger, ModifierMLkeras, ModifierMLModel, ModifierML, DNAModifierML Package: RNAmodR.RiboMethSeq Exports: ModRiboMethSeq, ModSetRiboMethSeq ExportMethods: plotDataByCoord, plotData, getDataTrack, findMod, aggregateData, settings<- ExportClasses: ModSetRiboMethSeq, ModRiboMethSeq Package: RNAprobR Exports: BED2txDb, GR2norm_df, bam2bedgraph, bedgraph2norm, comp, compdata, correct_oversaturation, dtcr, k2n_calc, norm2bedgraph, norm_df2GR, plotRNA, plotReads, readsamples, slograt, swinsor, swinsor_vector, winsor Package: RNAsense Exports: combineResults, getFC, getSwitch, outputGeneTables, plotSSGS Package: rnaseqcomp Exports: plot2TX, plotFC, plotNE, plotROC, plotSD, signalCalibrate ExportClasses: rnaseqcomp Package: RNASeqPower Exports: rnapower Package: RNASeqR Exports: All_Steps_Interface, All_Steps_Interface_CMD, CheckToolAll, RNASeqDifferentialAnalysis, RNASeqDifferentialAnalysis_CMD, RNASeqEnvironmentSet, RNASeqEnvironmentSet_CMD, RNASeqGoKegg, RNASeqGoKegg_CMD, RNASeqQualityAssessment, RNASeqQualityAssessment_CMD, RNASeqRParam, RNASeqRParam_Bam, RNASeqRParam_Sam, RNASeqReadProcess, RNASeqReadProcess_CMD, Update_Fastq_gz ExportClasses: RNASeqRParam_Sam, RNASeqRParam_Bam, RNASeqRParam Package: Rnits Exports: build.Rnits, calculateGCV, fit, getCID, getFitModel, getLR, getNormTwoChannel, getPval, getStat, plotResults, summarizeProbes, timeAlign, topData ExportMethods: summary ExportClasses: Rnits Package: roar Exports: RoarDataset, RoarDatasetFromFiles, RoarDatasetMultipleAPAFromFiles, RoarDatasetMultipleAPA ExportMethods: countPrePost, computeRoars, computePvals, computePairedPvals, totalResults, fpkmResults, countResults, standardFilter, pvalueFilter, pvalueCorrectFilter ExportClasses: RoarDataset, RoarDatasetMultipleAPA Package: ROC Exports: AUC, AUCi, dxrule.sca, pAUC, pAUCi, ROC, rocdemo.sca, trapezint ExportMethods: plot, points, lines ExportClasses: rocc Package: Roleswitch Exports: roleswitch, getSeedMatrix, diagnosticPlot Package: rols Exports: charIsCVParam, CVParam, olsVersion, olsLoaded, olsUpdated, isObsolete, isRoot, termSynonym, children, parents, ancestors, descendants, derivesFrom, partOf, as.Term.data.frame, as.Terms.data.frame, OlsSearch, olsSearch, olsRows, olsRows<-, allRows ExportMethods: show, [, [[, lapply, coerce, length, unique, Ontology, Ontologies, olsRoot, olsPrefix, olsDesc, olsTitle, olsStatus, olsNamespace, all.equal, termLabel, termPrefix, termNamespace, termOntology, termDesc, term, terms, termId, properties ExportClasses: CVParam, Term, Terms, Ontology, Ontologies, OlsSearch, Property, Properties Package: ROntoTools Exports: alpha1MR, alphaMLG, compute.fisher, compute.normalInv, keggPathwayGraphs, keggPathwayNames, nodeWeights, pDis, pe, peEdgeRenderInfo, peNodeRenderInfo, setEdgeWeights, setNodeWeights ExportMethods: plot, nodeWeights, Summary ExportClasses: peRes, pePathway, pDisRes, pDisPathway Package: ropls Exports: checkW4M, fromW4M, getEset, getLoadingMN, getMset, getPcaVarVn, getScoreMN, getSubsetVi, getSummaryDF, getVipVn, getWeightMN, imageF, opls, residuals, strF, tested, toW4M, view ExportMethods: view, tested, show, print, predict, plot, opls, getWeightMN, getVipVn, getSummaryDF, getSubsetVi, getScoreMN, getPcaVarVn, getMset, getLoadingMN, getEset, fitted, coef ExportClasses: oplsMultiDataSet, opls Package: RPA Exports: RPA.iteration, RPA.preprocess, calculate.rpa, collect.hyperparameters, d.update.fast, estimate.affinities, estimate.hyperparameters, frpa, get.probe.matrix, get.probe.parameters, get.probeset, hyperparameter.update, n.phylotypes.per.oligo, online.quantile, probe.parameters.tolist, probe.performance, probeplot, probetable, rpa, rpa.complete, rpa.fit, rpa.online, rpa.plot, rpa.summarize, rpaplot, sample.probeset, summarize.batch, summarize.batches, summarize.rpa, summarize.sum, summarize_probedata, updating.hyperparameters Package: RProtoBufLib Exports: LdFlags Package: RpsiXML Exports: parsePsimi25Interaction, parsePsimi25Complex, psimi25XML2Graph, list2Matrix, complexEntry2graph, buildPCHypergraph, separateXMLDataByExpt, HPRD.PSIMI25, BIOGRID.PSIMI25, MINT.PSIMI25, INTACT.PSIMI25, DIP.PSIMI25, MIPS.PSIMI25, MATRIXDB.PSIMI25, CORUM.PSIMI25, MPACT.PSIMI25, iListHandler, eListHandler, graphConverter, hyperGraphConverter, psimi25Hypergraph2GraphNEL, bait, prey, participant, confidenceValue, inhibitor, neutralComponent, pubmedID, null2na, getAbstractByPMID, xref, complexName, attributesList, members, validatePSIMI25 ExportMethods: abstract, availableXrefs, edgeLabel, hyperedgeNodes, show, initialize, translateID, interactorInfo, interactionType, complexes, uniprot, revInciMat, releaseDate, interactors, interactions, numInteractors, numInteractions, taxId, taxId<-, organismName, organismName<-, sourceDb, sourceDb<-, sourceId, sourceId<- ExportClasses: psimi25InteractionEntry, psimi25ComplexEntry, psimi25Interactor, psimi25Interaction, psimi25Complex, psimi25Experiment, psimi25Graph, psimi25Hypergraph, psimi25Source Package: rpx Exports: PXDataset, show, pxid, pxurl, pxtax, pxref, pxfiles, pxget, pxannounced ExportClasses: PXDataset Package: Rqc Exports: checkpoint, detectFileFormat, fromRRDNA, matdist, rqc, rqcCycleAverageQualityCalc, rqcCycleAverageQualityPcaCalc, rqcCycleAverageQualityPcaPlot, rqcCycleAverageQualityPlot, rqcCycleBaseCallsCalc, rqcCycleBaseCallsLinePlot, rqcCycleBaseCallsPlot, rqcCycleGCCalc, rqcCycleGCPlot, rqcCycleQualityBoxCalc, rqcCycleQualityBoxPlot, rqcCycleQualityCalc, rqcCycleQualityPlot, rqcFileHeatmap, rqcGroupCycleAverageQualityCalc, rqcGroupCycleAverageQualityPlot, rqcReadFrequencyCalc, rqcReadFrequencyPlot, rqcReadQualityBoxCalc, rqcReadQualityBoxPlot, rqcReadQualityCalc, rqcReadQualityPlot, rqcReadWidthCalc, rqcReadWidthPlot, rqcReport, rqcShinyReport, stats4trim, subsetByGroup, subsetByPair, toRRDNA ExportMethods: rqcQA, perReadWidth, perReadQuality, perReadFrequency, perFileTopReads, perFileInformation, perCycleQuality, perCycleBasecall ExportClasses: RqcResultSet Package: rqt Exports: rqt ExportMethods: results, phenotype, genotype, geneTestMeta, geneTest, covariates Package: rqubic Exports: combineBiclusts, readBiclusterResults, fcFilter, parseQubicRules, parseQubicChars, parseQubicBlocks, eSetDimName, writeQubicInputFile, quantileDiscretize, generateSeeds, quBicluster ExportMethods: BCcount, info, Svalue, RowxNumber, NumberxCol, features, featureNames, sampleNames, featureCount, BCfeatures, BCfeatureCount, conditions, conditionCount, BCconditions, BCconditionCount, parameter ExportClasses: QUBICBiclusterSet Package: rRDP Exports: rdp, trainRDP, removeRDP, GenClass16S, encode_Greengenes, decode_Greengenes, encode_RDP, decode_RDP, accuracy, confusionTable Package: RRHO Exports: RRHO, pvalRRHO, RRHOComparison Package: Rsamtools ExportMethods: length, names, [, [[, show, getSeq, seqinfo Package: rScudo Exports: ScudoResults, consensusDownSignatures, consensusUpSignatures, distMatrix, downSignatures, groupsAnnotation, scudoClassify, scudoCytoscape, scudoModel, scudoNetwork, scudoParams, scudoPlot, scudoTest, scudoTrain, selectedFeatures, upSignatures ExportClasses: ScudoResults Package: RSeqAn Exports: containment_test Package: RSVSim ExportMethods: simulateSV, estimateSVSizes, compareSV Package: RTCA Exports: alphaNames, repairAlphaName, alphaNames2Pos, rowcol2pos, factor2numeric, relevels, parseRTCA, combineRTCA, nearestTimeIndex, sliceRTCA, ratioTransform, smoothTransform, interpolationTransform, derivativeTransform, rgrTransform, plotGridEffect, controlView, plateView, spectramaxImport ExportMethods: actionTrack, actionTrack<-, timeUnit, timeUnit<-, startTime, startTime<-, getAction, addAction, rmAction, orderAction, updateAction, reset, expID, expID<-, timeline, timeline<-, timepoints, timepoints<-, plot ExportClasses: RTCAtimeline, RTCA Package: RTCGA Exports: boxplotTCGA, checkTCGA, convertPANCAN12, convertTCGA, downloadTCGA, expressionsTCGA, heatmapTCGA, infoTCGA, installTCGA, kmTCGA, mutationsTCGA, pcaTCGA, readTCGA, survivalTCGA, theme_RTCGA Package: RTCGAToolbox Exports: biocExtract, getBroadSubtypes, getCNGECorrelation, getDiffExpressedGenes, getFirehoseAnalyzeDates, getFirehoseData, getFirehoseDatasets, getFirehoseRunningDates, getGISTICPeaks, getMutationRate, getReport, getSurvival ExportMethods: updateObject, showResults, selectType, isEmpty, getData ExportClasses: FirehosemRNAArray, FirehoseMethylationArray, FirehoseGISTIC, FirehoseData, FirehoseCGHArray, DGEResult, CorResult Package: RTN Exports: tni.constructor, tna.plot.gsea1, tna.plot.gsea2, avs.plot1, avs.plot2, upgradeTNI, upgradeTNA ExportMethods: tni.preprocess, tni.permutation, tni.bootstrap, tni.dpi.filter, tni.get, tni.graph, tni.conditional, tni.gsea2, tni.area3, tni.regulon.summary, tni.prune, tni.replace.samples, tni2tna.preprocess, tna.mra, tna.gsea1, tna.gsea2, tna.overlap, tna.synergy, tna.shadow, tna.get, tna.graph, avs.vse, avs.evse, avs.pevse, avs.get ExportClasses: TNI, TNA, AVS Package: RTNduals Exports: mbrPlotDuals, mbrPlotInteraction ExportMethods: tni2mbrPreprocess, mbrPriorEvidenceTable, mbrGet, mbrAssociation ExportClasses: MBR Package: RTNsurvival Exports: hclust_semisupervised, tnsStratification ExportMethods: tnsSRE, tnsSRD, tnsPlotSRE, tnsPlotKmInteraction, tnsPlotKM, tnsPlotGSEA2, tnsPlotCoxInteraction, tnsPlotCox, tnsPlotCovariates, tnsKmInteraction, tnsKM, tnsInteraction, tnsGet, tnsGSEA2, tnsCoxInteraction, tnsCox, tnsAREA3, tni2tnsPreprocess ExportClasses: TNS Package: RTopper Exports: convertToDr, computeDrStat, runBatchGSE, combineGSE, adjustPvalGSE Package: rtracklayer Exports: genomeBrowsers, start, end, strand, start<-, end<-, width, width<-, ranges, values, GenomicData, GenomicSelection, score, score<-, as.data.frame, space, ucscGenomes, readGFFPragmas, sniffGFFVersion, GFFcolnames, readGFF, readGFFAsGRanges, BigWigSelection, GRangesForUCSCGenome, GRangesForBSGenome, summary, seqinfo, genome, genome<-, uri, Quickload, quickload, QuickloadGenome, organism, releaseDate, mcols, wigToBigWig, SeqinfoForBSGenome, SeqinfoForUCSCGenome, resource, path, FileForFormat, cleanupBigWigCache, viewURL, GFFFile, UCSCFile, BEDFile, WIGFile, ChainFile, FastaFile, GFF1File, GFF2File, GFF3File, BEDGraphFile, BED15File, GTFFile, GVFFile, BigWigFile, BigWigFileList, TwoBitFile, BEDPEFile ExportMethods: activeView, activeView<-, blocks, browseGenome, browserSession, browserSession<-, browserView, browserViews, close, export, export.bed, export.bed15, export.bedGraph, export.gff, export.gff1, export.gff2, export.gff3, export.ucsc, export.wig, export.bw, export.2bit, import, import.bed, import.bed15, import.bedGraph, import.gff, import.gff1, import.gff2, import.gff3, import.ucsc, import.wig, import.bw, import.chain, import.2bit, exportToTabix, track<-, track, trackNames, trackNames<-, getTable, tableNames, trackName, trackName<-, tableName, tableName<-, ucscTrackModes, ucscTrackModes<-, ucscSchema, coerce, initialize, show, summary, [, ucscTableQuery, genome, genome<-, chrom, chrom<-, range, range<-, visible, visible<-, liftOver, offset, reversed, nrow, formatDescription, referenceSequence, referenceSequence<-, asBED, asGFF, split, fileFormat, start, end, start<-, end<-, score, score<-, as.data.frame, space, mcols, strand, seqinfo, seqinfo<-, organism, releaseDate, getSeq ExportClasses: RTLFile, CompressedFile, GFFFile, UCSCFile, BEDFile, WIGFile, ChainFile, FastaFile, GFF1File, GFF2File, GFF3File, BEDGraphFile, BED15File, GTFFile, GVFFile, BigWigFile, BigWigFileList, TwoBitFile, RTLFileList, BEDPEFile, BrowserSession, BrowserView, BrowserViewList, UCSCSession, UCSCView, UCSCData, TrackLine, BasicTrackLine, GraphTrackLine, Bed15TrackLine, UCSCTrackModes, BigWigSelection, UCSCSchema, Quickload, QuickloadGenome Package: Rtreemix Exports: Pval.dist, kullback.leibler, L1.dist, cosin.dist, L2.norm, euclidian.dist, rank.cor.dist, get.tree.levels, comp.models, comp.models.levels, comp.trees, comp.trees.levels, stability.sim ExportMethods: initialize, print, show, Sample, Events, Patients, Description, sampleSize, eventsNum, Events<-, Patients<-, Description<-, Weights, Weights<-, WeightsCI, Resp, CompleteMat, Star, Trees, numTrees, getTree, getData, plot, Model, LogLikelihoods, WLikelihoods, getResp, SamplingMode, SamplingParam, GPS, gpsCI, SimPatterns, SamplingTimes, WaitingTimes, getModel, noDraws, fit, bootstrap, likelihoods, gps, confIntGPS, sim, generate, distribution ExportClasses: RtreemixData, RtreemixModel, RtreemixSim, RtreemixStats, RtreemixGPS Package: runibic Exports: BCUnibic, BCUnibicD, backtrackLCS, calculateLCS, cluster, pairwiseLCS, runiDiscretize, runibic, set_runibic_params, unisort Package: RUVcorr Exports: ECDFPlot, PCAPlot, RLEPlot, RUVNaiveRidge, assessQuality, background, calculateThreshold, compareRanks, correlationPlot, eigenvaluePlot, empNegativeControls, findWeights, genePlot, histogramPlot, is.optimizeParameters, is.simulateGEdata, optimizeParameters, plotDesign, plotThreshold, prioritise, simulateGEdata, wcor ExportMethods: simulateGEdata, empNegativeControls, RUVNaiveRidge ExportClasses: simulateGEdata, optimizeParameters, Weights, Threshold Package: RUVnormalize Exports: iterativeRUV, naiveRandRUV, naiveReplicateRUV, clScore, svdPlot Package: RUVSeq Exports: makeGroups ExportMethods: RUVg, RUVs, RUVr Package: RVS Exports: ComputeKinshipPropCoef, GeneDrop, GeneDropSim.allsubsets.fn, GeneDropSim.fn, GeneDropSimExcessSharing.fn, RVgene, RVsharing, SnpMatrixToCount, enrichmentPValue, get.psubset, multipleFamilyPValue, multipleVariantPValue, ped2trio, processPedigree Package: rWikiPathways Exports: downloadPathwayArchive, findPathwayIdsByLiterature, findPathwayIdsByText, findPathwayIdsByXref, findPathwayNamesByLiterature, findPathwayNamesByText, findPathwayNamesByXref, findPathwayUrlsByLiterature, findPathwayUrlsByText, findPathwayUrlsByXref, findPathwaysByLiterature, findPathwaysByText, findPathwaysByXref, getColoredPathway, getCurationTagNames, getCurationTags, getEveryCurationTag, getOntologyTermIds, getOntologyTermNames, getOntologyTerms, getPathway, getPathwayHistory, getPathwayIdsByCurationTag, getPathwayIdsByOntologyTerm, getPathwayIdsByParentOntologyTerm, getPathwayInfo, getPathwaysByCurationTag, getPathwaysByOntologyTerm, getPathwaysByParentOntologyTerm, getRecentChanges, getRecentChangesIds, getRecentChangesNames, getXrefList, listOrganisms, listPathwayIds, listPathwayNames, listPathwayUrls, listPathways, wikipathwaysAPI, wikipathwaysGET Package: S4Vectors Exports: aggregate.Vector, anyDuplicated.NSBS, anyDuplicated.Vector, anyDuplicated.Rle, as.character.LLint, as.data.frame.Vector, as.data.frame.DataTable, as.integer.LLint, as.list.Vector, as.logical.LLint, as.matrix.Vector, as.numeric.LLint, as.vector.Rle, cbind.DataFrame, diff.Rle, droplevels.Rle, droplevels.List, duplicated.DataTable, duplicated.Vector, head.DataTable, head.LLint, head.Vector, intersect.Vector, levels.Rle, mean.Rle, median.Rle, quantile.Rle, rbind.DataFrame, rev.Vector, rev.Rle, setdiff.Vector, setequal.Vector, sort.Vector, subset.Vector, summary.Vector, summary.Hits, summary.Rle, t.Hits, t.HitsList, tail.DataTable, tail.LLint, tail.Vector, transform.DataTable, transform.Vector, union.Vector, unique.DataTable, unique.Vector, window.LLint, window.Vector, setValidity2, new2, setMethods, coolcat, wmsg, .Call2, get_showHeadLines, get_showTailLines, printAtomicVectorInAGrid, isTRUEorFALSE, isSingleInteger, isSingleNumber, isSingleString, isSingleNumberOrNA, isSingleStringOrNA, recycleIntegerArg, recycleNumericArg, recycleLogicalArg, recycleCharacterArg, recycleArg, fold, is.LLint, as.LLint, LLint, normalizeSingleBracketSubscript, normalizeDoubleBracketSubscript, isSequence, toListOfIntegerVectors, orderIntegerPairs, matchIntegerPairs, selfmatchIntegerPairs, duplicatedIntegerPairs, orderIntegerQuads, matchIntegerQuads, selfmatchIntegerQuads, duplicatedIntegerQuads, safeExplode, svn.time, queryHits, subjectHits, queryLength, subjectLength, countQueryHits, countSubjectHits, Hits, SelfHits, selectHits, breakTies, remapHits, isSelfHit, isRedundantHit, Factor, List, pc, endoapply, mendoapply, SimpleList, HitsList, DataFrame, Pairs, FilterRules, FilterMatrix, classNameForDisplay, showAsCell, bindROWS, isConstant, isSorted, isStrictlySorted, NSBS, normalizeSingleBracketReplacementValue, extractROWS, replaceROWS, mergeROWS, extractCOLS, replaceCOLS, getListElement, setListElement, unstrsplit, ROWNAMES, as.env, metadata, metadata<-, parallelSlotNames, parallelVectorNames, elementMetadata, mcols, values, elementMetadata<-, mcols<-, values<-, rename, pcompare, sameAsPreviousROW, selfmatch, findMatches, countMatches, from, to, nLnode, nRnode, nnode, countLnodeHits, countRnodeHits, runLength, runLength<-, runValue, runValue<-, nrun, Rle, findRun, decode, runsum, runmean, runwtsum, runq, FactorToClass, unfactor, elementType, elementNROWS, isEmpty, pcompareRecursively, relistToClass, splitAsList, revElements, space, first, first<-, second, second<-, zipup, zipdown, expand, active, active<-, evalSeparately, subsetByFilter, params, filterRules, shiftApply ExportMethods: classNameForDisplay, showAsCell, bindROWS, isConstant, isSorted, isStrictlySorted, NSBS, normalizeSingleBracketReplacementValue, extractROWS, replaceROWS, getListElement, setListElement, unstrsplit, ROWNAMES, as.env, metadata, metadata<-, parallelSlotNames, parallelVectorNames, elementMetadata, mcols, values, elementMetadata<-, mcols<-, values<-, rename, pcompare, sameAsPreviousROW, selfmatch, findMatches, countMatches, from, to, nLnode, nRnode, nnode, countLnodeHits, countRnodeHits, runLength, runLength<-, runValue, runValue<-, nrun, Rle, findRun, runsum, runmean, runwtsum, runq, FactorToClass, unfactor, elementType, elementNROWS, isEmpty, pcompareRecursively, relistToClass, splitAsList, revElements, space, first, first<-, second, second<-, zipup, zipdown, expand, active, active<-, evalSeparately, subsetByFilter, params, filterRules, shiftApply, length, names, names<-, nrow, ncol, dim, NROW, NCOL, rownames, rownames<-, colnames, colnames<-, dimnames, dimnames<-, is.na, anyNA, as.logical, as.integer, as.numeric, as.complex, as.character, as.raw, as.factor, as.list, as.data.frame, as.matrix, as.table, [, [<-, subset, rev, rep, rep.int, c, append, ==, !=, <=, >=, <, >, Ops, Summary, !, match, duplicated, unique, anyDuplicated, %in%, order, sort, is.unsorted, rank, xtfrm, merge, t, by, transform, nchar, substr, substring, levels, levels<-, droplevels, [[, [[<-, $, $<-, lengths, split, eval, with, within, expand.grid, coerce, show, head, tail, var, cov, cor, sd, window, aggregate, na.omit, na.exclude, complete.cases, summary, cbind, rbind, lapply, sapply, Reduce, Filter, unlist, do.call, union, intersect, setdiff, setequal, xtabs, start, end, width, grep, grepl, updateObject ExportClasses: character_OR_NULL, vector_OR_factor, atomic, LLint, integer_OR_LLint, DataTable, NSBS, Annotated, DataTable_OR_NULL, Vector, vector_OR_Vector, Hits, SelfHits, SortedByQueryHits, SortedByQuerySelfHits, Rle, Factor, List, list_OR_List, SimpleList, HitsList, SortedByQueryHitsList, DataFrame, DFrame, Pairs, expression_OR_function, FilterRules, FilterMatrix 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: samExploreR Exports: samExplore, plotsamExplorer, exploreRep, exploreRob Package: sampleClassifier Exports: classifyProfile, classifyProfile.rnaseq, classifyProfile.svm, classifyProfile.rnaseq.svm, get.heatmap Package: sangerseqR Exports: peakAmpMatrix<-, peakPosMatrix<-, primarySeq<-, primarySeqID<-, secondarySeq<-, secondarySeqID<-, traceMatrix<-, PolyPeakParser, chromatogram, makeBaseCalls, peakAmpMatrix, peakPosMatrix, primarySeq, primarySeqID, read.abif, read.scf, readsangerseq, sangerseq, secondarySeq, secondarySeqID, setAllelePhase, traceMatrix ExportClasses: scf, sangerseq, abif Package: sapFinder Exports: dbCreator, runTandem, parserGear, reportCreator, easyRun Package: savR Exports: buildReports, clusterQualityGtN, clusters, correctedIntensities, cycles, directions, errorMetrics, extractionMetrics, flowcellLayout, location, pfBoxplot, pfClusters, plotFWHM, plotIntensity, plotQGT30, qualityHeatmap, qualityMetrics, reads, run, savR, tileMetrics Package: SBGNview Exports: outputFile<-, SBGNview, changeDataId, changeIds, downloadSbgnFile, findPathways, getMolList, highlightArcs, highlightNodes, highlightPath, loadMappingTable, outputFile, renderSbgn, sbgnNodes Package: SBMLR Exports: readSBML, readSBMLR, saveSBML, saveSBMLR, sim, S4toS3 Package: SC3 Exports: consensus_matrix, get_de_genes, get_marker_genes, get_outl_cells, get_processed_dataset, norm_laplacian, reindex_clusters, sc3, sc3_calc_biology, sc3_calc_consens, sc3_calc_dists, sc3_calc_transfs, sc3_estimate_k, sc3_export_results_xls, sc3_interactive, sc3_kmeans, sc3_plot_cluster_stability, sc3_plot_consensus, sc3_plot_de_genes, sc3_plot_expression, sc3_plot_markers, sc3_plot_silhouette, sc3_prepare, sc3_run_svm Package: Scale4C ExportMethods: calculateFingerprintMap, calculateScaleSpace, findSingularities, outputScaleSpaceTree, importBasic4CseqData, addPointsOfInterest, plotInflectionPoints, plotTesselation, plotTraceback, Scale4C, viewpoint, viewpoint<-, viewpointChromosome, viewpointChromosome<-, pointsOfInterest, pointsOfInterest<-, rawData, rawData<-, scaleSpace, scaleSpace<-, singularities, singularities<- ExportClasses: Scale4C Package: scAlign Exports: PlotTSNE, gaussianKernel, scAlign, scAlignCreateObject, scAlignMulti, scAlignOptions Package: SCAN.UPC Exports: SCAN, SCANfast, UPC, UPCfast, SCAN_TwoColor, UPC_TwoColor, UPC_RNASeq, UPC_RNASeq_Single, UPC_Generic, UPC_Generic_ExpressionSet, ParseMetaFromGtfFile, InstallBrainArrayPackage, BatchAdjust, BatchAdjustFromFile Package: scater Exports: bootstraps<-, fpkm<-, norm_exprs<-, stand_exprs<-, addPerCellQC, addPerFeatureQC, aggregateAcrossCells, aggregateAcrossFeatures, annotateBMFeatures, bootstraps, calculateAverage, calculateCPM, calculateDiffusionMap, calculateFPKM, calculateMDS, calculatePCA, calculateTPM, calculateTSNE, calculateUMAP, computeLibraryFactors, fpkm, getBMFeatureAnnos, getExplanatoryPCs, getVarianceExplained, isOutlier, librarySizeFactors, logNormCounts, mockSCE, multiplot, nexprs, norm_exprs, normalizeCounts, numDetectedAcrossCells, numDetectedAcrossFeatures, perCellQCMetrics, perFeatureQCMetrics, plotColData, plotDiffusionMap, plotDots, plotExplanatoryPCs, plotExplanatoryVariables, plotExpression, plotHeatmap, plotHighestExprs, plotMDS, plotPCASCE, plotPlatePosition, plotRLE, plotReducedDim, plotRowData, plotScater, plotTSNE, plotUMAP, quickPerCellQC, readSparseCounts, retrieveCellInfo, retrieveFeatureInfo, runColDataPCA, runDiffusionMap, runMDS, runTSNE, runUMAP, stand_exprs, sumCountsAcrossCells, sumCountsAcrossFeatures, toSingleCellExperiment, uniquifyFeatureNames, updateSCESet ExportMethods: sumCountsAcrossFeatures, sumCountsAcrossCells, runPCA, plotPCA, perFeatureQCMetrics, perCellQCMetrics, numDetectedAcrossFeatures, numDetectedAcrossCells, normalizeCounts, nexprs, logNormCounts, librarySizeFactors, getVarianceExplained, calculateUMAP, calculateTSNE, calculateTPM, calculatePCA, calculateMDS, calculateDiffusionMap, calculateCPM, calculateAverage, bootstraps, aggregateAcrossCells ExportClasses: SCESet Package: scBFA Exports: BinaryPCA, diagnose, getGeneExpr, getLoading, getScore, scBFA, scNoiseSim Package: SCBN Exports: Iter_optimal, MediancalcNorm, SCBN, generateDataset, sageTestNew Package: scDblFinder Exports: doubletThresholding, getArtificialDoublets, overcluster, plotROCs, rankTrans, resplitClusters, scDblFinder Package: scDD Exports: preprocess, results, scDD, sideViolin, simulateSet, testKS Package: scde Exports: bwpca, knn.error.models, make.pagoda.app, pagoda.cluster.cells, pagoda.effective.cells, pagoda.gene.clusters, pagoda.pathway.wPCA, pagoda.reduce.loading.redundancy, pagoda.reduce.redundancy, pagoda.show.pathways, pagoda.subtract.aspect, pagoda.top.aspects, pagoda.varnorm, pagoda.view.aspects, scde.browse.diffexp, scde.error.models, scde.expression.difference, scde.expression.magnitude, scde.expression.prior, scde.failure.probability, scde.fit.models.to.reference, scde.posteriors, scde.test.gene.expression.difference, show.app, winsorize.matrix, clean.counts, clean.gos Package: scds Exports: bcds, cxds, cxds_bcds_hybrid Package: scFeatureFilter Exports: bin_scdata, calculate_cvs, correlate_windows, correlations_to_densities, define_top_genes, determine_bin_cutoff, filter_expression_table, get_mean_median, plot_correlations_distributions, plot_mean_variance, plot_metric, plot_top_window_autocor, sc_feature_filter Package: scfind Exports: buildCellIndex, buildCellTypeIndex, findCell, findCellType Package: scGPS Exports: CORE_bagging, CORE_clustering, CORE_subcluster, PCA, PrinComp_cpp, annotate_clusters, bootstrap_parallel, bootstrap_prediction, calcDist, calcDistArma, clustering, clustering_bagging, distvec, find_markers, find_optimal_stability, find_stability, mean_cpp, new_scGPS_object, new_summarized_scGPS_object, plot_CORE, plot_optimal_CORE, plot_reduced, predicting, rand_index, rcpp_Eucl_distance_NotPar, rcpp_parallel_distance, reformat_LASSO, sub_clustering, subset_cpp, summary_accuracy, summary_deviance, summary_prediction_lasso, summary_prediction_lda, tSNE, top_var, tp_cpp, training, var_cpp Package: schex Exports: make_hexbin, make_hexbin_label, plot_hexbin_density, plot_hexbin_feature, plot_hexbin_gene, plot_hexbin_interact, plot_hexbin_meta ExportMethods: plot_hexbin_meta, plot_hexbin_interact, plot_hexbin_gene, plot_hexbin_feature, plot_hexbin_density, make_hexbin_label, make_hexbin 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: scmap Exports: getSankey, indexCell, indexCluster, scmapCell, scmapCell2Cluster, scmapCluster, selectFeatures, setFeatures Package: scMerge Exports: eigenMatMult, eigenResidop, fastRUVIII, ruvSimulate, scMerge, scRUVIII, scRUVg, scReplicate, scSEGIndex, sce_cbind Package: scmeth Exports: bsConversionPlot, chromosomeCoverage, coverage, cpgDensity, cpgDiscretization, downsample, featureCoverage, mbiasplot, methylationDist, readmetrics, repMask, report Package: SCnorm Exports: SCnorm, getCounts, getSlopes, plotCountDepth, plotWithinFactor, results, scaleNormMultCont Package: scone Exports: CLR_FN, DESEQ_FN, FQT_FN, FQ_FN, SCRAN_FN, SUM_FN, SconeExperiment, TMM_FN, UQ_FN, biplot_color, biplot_interactive, estimate_ziber, factor_sample_filter, fast_estimate_ziber, impute_expectation, impute_null, lm_adjust, make_design, metric_sample_filter, sconeReport, scone_easybake, score_matrix, simple_FNR_params ExportMethods: select_methods, scone, get_scores, get_score_ranks, get_qc, get_poscon, get_params, get_normalized, get_negconruv, get_negconeval, get_design, get_bio, get_batch, SconeExperiment ExportClasses: SconeExperiment Package: Sconify Exports: FcsToTibble, Fnn, GetKnnDe, GetMarkerNames, ImputeTesting, MakeHist, MakeKnnList, MeaningOfLife, ParseMarkers, PostProcessing, ProcessMultipleFiles, QuantNormalizeElements, SconeValues, SplitFile, StringToNumbers, SubsampleAndTsne, TsneVis Package: scoreInvHap Exports: certainty, classifSNPs, classifSNPsImpute, classification, diffscores, maxscores, numSNPs, plotCallRate, plotScores, propSNPs, scoreInvHap, scores ExportMethods: propSNPs ExportClasses: scoreInvHapRes Package: scPCA Exports: scPCA Package: scPipe Exports: QC_metrics<-, UMI_dup_info<-, demultiplex_info<-, gene_id_type<-, QC_metrics, QC_metrics.sce, UMI_dup_info, UMI_dup_info.sce, anno_import, anno_to_saf, calculate_QC_metrics, convert_geneid, create_processed_report, create_report, create_sce_by_dir, demultiplex_info, demultiplex_info.sce, detect_outlier, gene_id_type, gene_id_type.sce, get_ercc_anno, get_genes_by_GO, get_read_str, organism.sce, plot_QC_pairs, plot_UMI_dup, plot_demultiplex, plot_mapping, remove_outliers, sc_count_aligned_bam, sc_demultiplex, sc_demultiplex_and_count, sc_detect_bc, sc_exon_mapping, sc_gene_counting, sc_trim_barcode ExportMethods: organism, gene_id_type, demultiplex_info, UMI_dup_info, QC_metrics, organism<-, gene_id_type<-, demultiplex_info<-, UMI_dup_info<-, QC_metrics<- Package: scran Exports: DM, bootstrapCluster, buildKNNGraph, buildSNNGraph, calculateSumFactors, cleanSizeFactors, clusterModularity, combineCV2, combineMarkers, combinePValues, combineVar, computeSpikeFactors, computeSumFactors, convertTo, correlateGenes, correlateNull, correlatePairs, cyclone, denoisePCA, denoisePCANumber, doubletCells, doubletCluster, findMarkers, fitTrendCV2, fitTrendPoisson, fitTrendVar, getClusteredPCs, getDenoisedPCs, getTopHVGs, getTopMarkers, modelGeneCV2, modelGeneCV2WithSpikes, modelGeneVar, modelGeneVarByPoisson, modelGeneVarWithSpikes, neighborsToKNNGraph, neighborsToSNNGraph, pairwiseBinom, pairwiseTTests, pairwiseWilcox, quickCluster, quickSubCluster, sandbag, scaledColRanks ExportMethods: sandbag, quickSubCluster, quickCluster, modelGeneVarWithSpikes, modelGeneVarByPoisson, modelGeneVar, modelGeneCV2WithSpikes, modelGeneCV2, getDenoisedPCs, findMarkers, doubletCluster, doubletCells, cyclone, correlatePairs, calculateSumFactors, buildSNNGraph, buildKNNGraph Package: scRecover Exports: countsSampling, estDropoutNum, normalization, scRecover Package: scruff Exports: alignRsubread, countUMI, demultiplex, gview, qcplots, rview, scruff, tenxBamqc Package: scTensor Exports: cellCellSimulate, newCCSParams, convertToNCBIGeneID ExportMethods: cellCellSetting, cellCellRanks, cellCellDecomp, cellCellReport, getParam, setParam<- Package: scTGIF Exports: settingTGIF, calcTGIF, reportTGIF Package: SDAMS Exports: createSEFromMatrix, createSEFromCSV, SDA Package: segmentSeq ExportMethods: dim, [, show ExportClasses: alignmentData Package: SELEX Exports: selex.kmerPSFM, selex.fastqPSFM, selex.getAttributes, selex.affinities, selex.loadAnnotation, selex.defineSample, selex.config, selex.infogainSummary, selex.mmSummary, selex.run, selex.summary, selex.countSummary, selex.split, selex.sampleSummary, selex.sample, selex.jvmStatus, selex.setwd, selex.revcomp, selex.mmProb, selex.counts, selex.mm, selex.infogain, selex.kmax, selex.seqfilter, selex.getSeqfilter, selex.exampledata, selex.getRound0, selex.saveAnnotation, selex.samplePSFM Package: semisup Exports: estim.nbinom, estim.zinb, fit.nbinom, fit.norm, fit.wrap, fit.zinb, mixtura, resam.lrts, scrutor Package: SEPIRA Exports: LimmaFn, sepiraInfNet, sepiraRegAct Package: seq2pathway Exports: addDescription, FisherTest_GO_BP_MF_CC, FisherTest_MsigDB, gene2pathway_test, runseq2gene, runseq2pathway, plotTop10 Package: SeqArray Exports: .onAttach, .Last.lib ExportMethods: seqClose, seqSetFilter, granges, ref, alt, qual, filt, header, fixed, info, geno, colData, rowRanges ExportClasses: SeqVarGDSClass Package: seqCAT Exports: calculate_similarity, compare_many, compare_profiles, create_profile, create_profiles, filter_duplicates, filter_variants, list_cosmic, list_variants, plot_heatmap, plot_impacts, plot_variant_list, read_cosmic, read_profile, read_profiles, write_profile, write_profiles Package: seqcombo Exports: geom_genotype, geom_hybrid, hybrid_plot, plot_grid, seqdiff, set_layout, simplot ExportMethods: show, plot Package: SeqGSEA Exports: DENBStat4GSEA, DENBStatPermut4GSEA, DENBTest, DEpermutePval, DSpermute4GSEA, DSpermutePval, DSresultExonTable, DSresultGeneTable, GSEAresultTable, GSEnrichAnalyze, calES, calES.perm, convertEnsembl2Symbol, convertSymbol2Ensembl, estiExonNBstat, estiGeneNBstat, exonID, exonTestability, geneID, geneList, genePermuteScore, geneScore, geneSetDescs, geneSetNames, geneSetSize, geneTestability, genpermuteMat, getGeneCount, label, loadExonCountData, loadGenesets, newGeneSets, newReadCountSet, normES, normFactor, plotES, plotGeneScore, plotSig, plotSigGeneSet, rankCombine, runDESeq, runSeqGSEA, scoreNormalization, signifES, size, subsetByGenes, topDEGenes, topDSExons, topDSGenes, topGeneSets, writeSigGeneSet, writeScores, runSeqGSEA ExportMethods: counts, counts<-, [ ExportClasses: SeqGeneSet, ReadCountSet Package: seqLogo Exports: seqLogo, makePWM ExportMethods: plot, summary, show ExportClasses: pwm Package: seqPattern ExportMethods: motifScanHits, motifScanScores, getPatternOccurrenceList, plotPatternDensityMap, plotPatternOccurrenceAverage, plotMotifDensityMap, plotMotifOccurrenceAverage, plotMotifScanScores Package: seqplots Exports: MotifSetup, add_local_file, getPlotSetArray, getREF, import.narrowPeak, plot, plotAverage, plotHeatmap, run ExportClasses: PlotSetPair, PlotSetList, PlotSetArray, MotifSetup Package: seqsetvis Exports: append_ynorm, applySpline, calc_norm_factors, centerAtMax, centerFixedSizeGRanges, clusteringKmeans, clusteringKmeansNestedHclust, col2hex, crossCorrByRle, easyLoad_bed, easyLoad_broadPeak, easyLoad_narrowPeak, fragLen_calcStranded, fragLen_fromMacs2Xls, ggellipse, harmonize_seqlengths, prepare_fetch_GRanges, quantileGRangesWidth, safeBrew, ssvFactorizeMembTable, ssvFeatureBars, ssvFeatureBinaryHeatmap, ssvFeatureEuler, ssvFeaturePie, ssvFeatureVenn, ssvFetchBam, ssvFetchBamPE, ssvFetchBigwig, ssvFetchGRanges, ssvFetchSignal, ssvMakeMembTable, ssvOverlapIntervalSets, ssvSignalBandedQuantiles, ssvSignalClustering, ssvSignalHeatmap, ssvSignalLineplot, ssvSignalLineplotAgg, ssvSignalScatterplot, viewGRangesWinSample_dt, viewGRangesWinSummary_dt ExportMethods: ssvMakeMembTable Package: SeqSQC Exports: IBDCheck, IBDRemove, Inbreeding, LoadVfile, MissingRate, PCACheck, RenderReport, SeqOpen, SeqSQC, SexCheck, plotQC, problemList, sampleQC ExportMethods: gdsfile, QCresult, gdsfile<-, QCresult<- ExportClasses: SeqSQC Package: seqTools Exports: ascii2char, countDnaKmers, countFastaKmers, countGenomeKmers, countSpliceKmers, char2ascii, kMerIndex, phredTable, fastqq, fastqKmerLocs, fastqKmerSubsetLocs, phredDist, plotPhredDist, plotPhredQuant, phredQuantiles, revCountDnaKmers, simFastqqRunTimes, sim_fq, trimFastq, writeFai, writeSimFastq, writeSimContFastq ExportMethods: cbDistMatrix, collectTime, collectDur, gcContent, gcContentMatrix, getGCcontent, fileNames, getK, kmerCount, kmerSvd, maxSeqLen, meltDownK, mergedPhred, mergedPhredQuantiles, mergeFastqq, nFiles, nNnucs, nReads, nucFreq, phred, plotGCcontent, plotKmerCount, plotMergedPhredQuant, plotNucCount, plotNucFreq, probeLabel, probeLabel<-, propPhred, seqLen, seqLenCount ExportClasses: Fastqq Package: SeqVarTools Exports: SeqVarData, SeqVarIterator, SeqVarBlockIterator, SeqVarRangeIterator, SeqVarWindowIterator, SeqVarListIterator, setVariantID ExportMethods: show, sampleData, sampleData<-, variantData, variantData<-, validateSex, granges, variantFilter, lastFilter, lastFilter<-, variantBlock, variantRanges, iterateFilter, resetIterator, currentRanges, currentVariants, applyMethod, refChar, altChar, nAlleles, isVariant, isSNV, getGenotype, getGenotypeAlleles, refDosage, altDosage, alleleDosage, expandedAltDosage, expandedVariantIndex, variantInfo, getVariableLengthData, imputedDosage, titv, alleleFrequency, alleleCount, minorAlleleCount, missingGenotypeRate, heterozygosity, hethom, homozygosity, meanBySample, countSingletons, pca, hwe, inbreedCoeff, mendelErr, duplicateDiscordance, alternateAlleleDetection, refFrac, refFracOverHets, refFracPlot, regression, chromWithPAR ExportClasses: SeqVarData, SeqVarIterator, SeqVarBlockIterator, SeqVarRangeIterator, SeqVarWindowIterator, SeqVarListIterator Package: sesame Exports: IG<-, II<-, IR<-, ctl<-, oobG<-, oobR<-, pval<-, BetaValueToMValue, DML, DMR, IG, II, IR, MValueToBetaValue, RGChannelSetToSigSets, SNPcheck, SigSet, SigSetList, SigSetListFromIDATs, SigSetListFromPath, SigSetToRatioSet, SigSetsToRGChannelSet, SignalSet, bisConversionControl, buildControlMatrix450k, cnSegmentation, ctl, detectionPfixedNorm, detectionPnegEcdf, detectionPnegNorm, detectionPnegNormGS, detectionPnegNormTotal, detectionPoobEcdf, detectionZero, diffRefSet, dyeBiasCorr, dyeBiasCorrMostBalanced, dyeBiasCorrTypeINorm, estimateLeukocyte, getAFTypeIbySumAlleles, getBetas, getNormCtls, getProbesByGene, getProbesByRegion, getProbesByTSS, getRefSet, getSegment, getSexInfo, inferEthnicity, inferSex, inferSexKaryotypes, inferTypeIChannel, initFileSet, makeExampleSeSAMeDataSet, makeExampleTinyEPICDataSet, mapFileSet, meanIntensity, noob, noobsb, oobG, oobR, openSesame, openSesameToFile, pOOBAH, parseGEOSignalABFile, predictAgeHorvath353, predictAgePheno, predictAgeSkinBlood, probeNames, pval, readFileSet, readIDATpair, searchIDATprefixes, sesameQC, sesamize, signalR6toS4, sliceFileSet, subsetSignal, topLoci, topSegments, totalIntensities, totalIntensityZscore, visualizeGene, visualizeProbes, visualizeRegion, visualizeSegments ExportMethods: show ExportClasses: SigSetList, SigSet Package: SEtools Exports: crossHm, log2FC, meltSE, mergeSEs, resetAllSEtoolsOptions, sehm, sortRows Package: sevenbridges Exports: %>>%, response<-, AWSInstanceTypeRequirement, AnyRequirement, App, Auth, Binding, CCBList, CLB, COB, CPURequirement, CWL, CommandInputParameter, CommandInputSchema, CommandLineBinding, CommandLineTool, CommandOutputBinding, CommandOutputParameter, CommandOutputSchema, ComplexEnum, CreateFileRequirement, DSCList, DatatypeEnum, DockerRequirement, EnvVarRequirement, EnvironmentDef, EnvironmentDefList, Expression, ExpressionEngineRequirement, ExpressionTool, FS, File, FileDef, FileDefList, FileList, Files, FilesList, Flow, IPList, InPar, InputParameter, InputParameterList, InputSchema, ItemArray, MemRequirement, Metadata, OPList, OutPar, OutputParameter, OutputParameterList, OutputSchema, Parameter, PrimitiveEnum, Process, ProcessRequirement, ProcessRequirementList, SBGWorkflow, ScatterFeatureRequirement, Schema, SchemaDef, SchemaDefList, SchemaList, SubworkflowFeatureRequirement, Tool, Workflow, WorkflowOutputParameter, WorkflowOutputParameterList, WorkflowStep, WorkflowStepInput, WorkflowStepInputList, WorkflowStepList, WorkflowStepOutput, WorkflowStepOutputList, access_level, addIdNum, add_tag, age_at_diagnosis, aliquot_id, aliquot_uuid, analysis_uuid, anyReq, api, appType, argslist, asList, aws, batch, case_id, case_uuid, cli_list_projects, cli_list_tags, cli_upload, convert_app, cpu, data_format, data_subtype, data_type, days_to_death, delete, disease_type, docker, download, enum, ethnicity, experimental_strategy, fileDef, file_extension, file_segment_number, gdc_file_uuid, gender, getTaskHook, get_cwl_class, get_token, get_uploader, input, input_matrix, investigation, is_commandlinetool, is_workflow, library_id, link, link_what, mem, misc_get_token, misc_get_uploader, misc_make_metadata, misc_upload_cli, output, output_matrix, paired_end, platform, platform_unit_id, primary_site, project_details, project_members, quality_scale, race, reference_genome, requirements, response, sample_id, sample_type, sample_uuid, sbg_get_env, sbg_set_env, setTaskHook, set_tag, set_test_env, test_tool_bunny, test_tool_cwlrun, test_tool_rabix, upload_complete_all, upload_complete_part, upload_delete, upload_info, upload_info_part, upload_init, vital_status ExportMethods: link_what, link, +, %>>% ExportClasses: enum, characterORCommandLineBindingList, WorkflowStepOutputList, WorkflowStepOutput, WorkflowStepList, WorkflowStepInputList, WorkflowStepInput, WorkflowStep, WorkflowOutputParameterList, WorkflowOutputParameter, Workflow, Tool, SubworkflowFeatureRequirement, SchemaList, SchemaDefList, SchemaDef, Schema, ScatterFeatureRequirement, SBGWorkflow, ProcessRequirementList, ProcessRequirement, Process, PrimitiveSingleEnum, Parameter, OutputSchema, OutputParameterList, OutputParameter, Metadata, MemRequirement, ItemArray, InputSchema, InputParameterList, InputParameter, FilesList, Files, FileList, FileDefList, FileDef, File, ExpressionTool, ExpressionEngineRequirement, Expression, EnvironmentDefList, EnvironmentDef, EnvVarRequirement, DockerRequirement, DatatypeSingleEnum, DSCList, CreateFileRequirement, ComplexSingleEnum, CommandOutputSchema, CommandOutputParameter, CommandOutputBinding, CommandLineTool, CommandLineBinding, CommandInputSchema, CommandInputParameter, CWL, CPURequirement, Binding, Auth, AnyRequirement, AWSInstanceTypeRequirement Package: sevenC Exports: addCor, addCovCor, addCovToGR, addInteractionSupport, addMotifScore, addStrandCombination, getCisPairs, parseLoopsRao, parseLoopsTang, predLoops, prepareCisPairs Package: SGSeq Exports: analyzeFeatures, analyzeVariants, annotate, convertToSGFeatures, convertToTxFeatures, exportFeatures, findSGVariants, getBamInfo, getSGFeatureCounts, getSGVariantCounts, importTranscripts, makeSGFeatureCounts, makeVariantNames, mergeTxFeatures, plotCoverage, plotFeatures, plotSpliceGraph, plotVariants, predictTxFeatures, predictVariantEffects, processTerminalExons, TxFeatures, SGFeatures, SGVariants, SGFeatureCounts, SGVariantCounts ExportMethods: type<-, txName<-, geneName<-, splice5p<-, splice3p<-, featureID<-, geneID<-, from<-, to<-, segmentID<-, eventID<-, variantID<-, closed5p<-, closed3p<-, closed5pEvent<-, closed3pEvent<-, variantType<-, variantName<-, featureID5p<-, featureID3p<-, featureID5pEvent<-, featureID3pEvent<-, counts<-, FPKM<-, variantFreq<-, type, txName, geneName, splice5p, splice3p, featureID, geneID, from, to, segmentID, eventID, variantID, closed5p, closed3p, closed5pEvent, closed3pEvent, variantType, variantName, featureID5p, featureID3p, featureID5pEvent, featureID3pEvent, counts, FPKM, variantFreq, updateObject Package: SharedObject Exports: .getProperty, .removeObject, .setProperty, getCopyOnWrite, getDataInfo, getSharedCopy, getSharedObjectOptions, getSharedProperties, getSharedSubset, is.altrep, is.shared, setCopyOnWrite, setSharedCopy, setSharedObjectOptions, setSharedSubset, share Package: shinyMethyl Exports: runShinyMethyl, getGreenControls, getRedControls, orderByName, shinySummarize, getPCA, shinyMethylSet ExportMethods: combine, shinySummarize, show, getBeta, getM, getMeth, getUnmeth, getCN, pData, sampleNames ExportClasses: shinyMethylSet Package: shinyTANDEM Exports: shinyTANDEM Package: ShortRead Exports: pData, phenoData, varLabels, varMetadata ExportMethods: show, coerce, dim, length, [, [<-, [[, alphabetFrequency, alphabet, coverage, encoding, narrow, reverse, reverseComplement, strand, trimLRPatterns, width, append, rbind, %in%, c, lapply, sapply Package: SIAMCAT Exports: associations<-, data_split<-, eval_data<-, filt_feat<-, label<-, meta<-, model_list<-, norm_feat<-, orig_feat<-, physeq<-, pred_matrix<-, accessSlot, add.meta.pred, assoc_param, associations, check.associations, check.confounders, create.data.split, create.label, data_split, eval_data, evaluate.predictions, feature_type, feature_weights, filt_feat, filt_params, filter.features, filter.label, get.filt_feat.matrix, get.norm_feat.matrix, get.orig_feat.matrix, label, make.predictions, meta, model.evaluation.plot, model.interpretation.plot, model_list, model_type, models, norm_feat, norm_params, normalize.features, orig_feat, physeq, pred_matrix, read.label, read.lefse, select.samples, siamcat, siamcat.to.lefse, siamcat.to.maaslin, summarize.features, train.model, validate.data, weight_matrix ExportClasses: siamcat Package: SICtools Exports: snpDiff, indelDiff Package: sigaR Exports: cghCall2cghSeg, cghCall2maximumSubset, cghCall2order, cghCall2subset, cghCall2weightedSubset, cghSeg2order, cghSeg2subset, cghSeg2weightedSubset, cisEffectPlot, cisEffectTable, cisEffectTest, cisEffectTune, CNGEheatmaps, entropyTest, expandMatching2singleIDs, ExpressionSet2order, ExpressionSet2subset, ExpressionSet2weightedSubset, getSegFeatures, hdEntropy, hdMI, matchAnn2Ann, matchCGHcall2ExpressionSet, merge2cghCalls, merge2ExpressionSets, mutInfTest, nBreakpoints, pathway1sample, pathway1sample, pathwayPlot, profilesPlot, RCMestimation, RCMrandom, RCMtest, splitMatchingAtBreakpoints, uniqGenomicInfo ExportMethods: RCMrandom, summary ExportClasses: cisTest, entTest, miTest, pathwayFit, rcmFit, rcmTest Package: SigCheck Exports: sigCheck, sigCheckRandom, sigCheckPermuted, sigCheckKnown, sigCheckPlot, sigCheckAll ExportClasses: SigCheckObject Package: SigFuge Exports: SFfigure, SFlabels, SFnormalize, SFpval Package: siggenes Exports: args.ebam, args.finda0, args.sam, ebam, ebam2excel, ebam2html, find.a0, fudge2, help.ebam, help.finda0, help.sam, link.genes, link.siggenes, list.siggenes, pi0.est, plotArguments, sam, sam2excel, sam2html, sam.plot2, d.stat, cat.stat, wilc.stat, z.ebam, cat.ebam, wilc.ebam, z.find, denspr, rowWilcoxon, rowRanksWilc, na.handling, nclass.wand, findDelta, qvalue.cal, chisqClass, chisq.ebam, chisq.stat, trend.stat, trend.ebam, md.plot, limma2sam, limma2ebam, samControl, ebamControl, fuzzy.stat, fuzzy.ebam ExportMethods: show, print, plot, summary, identify ExportClasses: SAM, EBAM, FindA0, sumSAM, sumEBAM Package: sights Exports: normLoess, normMedFil, normR, normRobZ, normSPAWN, normSights, normZ, plot3d, plotAutoco, plotBox, plotHeatmap, plotHist, plotIGFit, plotScatter, plotSights, statFDR, statRVM, statSights, statT Package: signatureSearch Exports: drugs<-, append2H5, build_custom_db, comp_fea_res, create_empty_h5, drug_cell_ranks, drugs, dsea_GSEA, dsea_hyperG, dtnetplot, enrichGO2, enrichKEGG2, enrichMOA, feaResult, gctx2h5, gessResult, gess_cmap, gess_cor, gess_fisher, gess_gcmap, gess_lincs, gess_res_vis, get_targets, gseGO2, gseKEGG2, mabsGO, mabsKEGG, matrix2h5, moa_conn, parse_gctx, qSig, rand_query_ES, readHDF5chunk, result, sim_score_grp, tsea_dup_hyperG, tsea_mGSEA, tsea_mabs ExportMethods: tail, show, head, dim ExportClasses: qSig, gessResult, feaResult Package: signeR Exports: genOpportunityFromGenome, genCountMatrixFromVcf, signeR, BICboxplot ExportMethods: setSamples, setMutations, Normalize, Reorder_signatures, Reorder_samples, Reorder_mutations, Average_sign, Median_sign, Average_exp, Median_exp, Paths, SignPlot, SignHeat, ExposureBoxplot, ExposureBarplot, ExposureHeat, Classify, DiffExp ExportClasses: SignExp Package: signet Exports: nullDist, searchSubnet, testSubnet, writeXGMML ExportMethods: summary, show, plot, initialize, [[, [ ExportClasses: SignetList, Signet Package: SigsPack Exports: bootstrap_mut_catalogues, create_mut_catalogues, decomposeQP, get_context_freq, normalize, plot_bootstrapped_exposure, signature_exposure, summarize_exposures, vcf2mut_cat Package: sigsquared ExportMethods: ensembleAdjustable, analysisPipeline, getDirect, getThresholds, getGenes, getNGenes, setGeneSignature, setDirect, setThresholds, setGenes ExportClasses: geneSignature 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: SIMAT Exports: getEIC, getPeak, getPeakScore, getRI, getRIStandard, getScore, getTarget, getTargetTable, optFrag, plotEIC, plotTIC, putTargetTable, readCDF, readMSL, writeMSL, writeResult Package: SimBindProfiles Exports: eSetScatterPlot, findBoundCutoff, increasedBindingRegions, pairwiseRegions, plotBoundProbes, probeAnnoFromESet, probeLengthPlot, readSgrFiles, threewayRegions, compensationRegions Package: SIMD Exports: EMalgorithm, EMtest, emalgth, emalgth1, probBinom Package: similaRpeak Exports: MetricFactory, similarity Package: SIMLR Exports: CIMLR, CIMLR_Estimate_Number_of_Clusters, SIMLR, SIMLR_Estimate_Number_of_Clusters, SIMLR_Feature_Ranking, SIMLR_Large_Scale Package: simpleaffy ExportMethods: [, avbg, calculated.from, calls, fc, get.array.subset, group, maxbg, means, members, minbg, pData, percent.present, plot, qc, qcProbes, ratios, sfs, spikeInProbes, target, tt ExportClasses: PairComp, QCStats Package: simulatorZ Exports: cvSubsets, funCV, geneFilter, getTrueModel, plusMinus, masomenos, simBootstrap, simData, simTime, zmatrix, rowCoxTests Package: SingleCellExperiment Exports: altExp<-, altExpNames<-, altExps<-, cpm<-, factorData<-, featureLoadings<-, int_colData<-, int_elementMetadata<-, int_metadata<-, isSpike<-, logcounts<-, normcounts<-, reducedDim<-, reducedDimNames<-, reducedDims<-, sampleFactors<-, tpm<-, weights<-, LinearEmbeddingMatrix, SingleCellExperiment, altExp, altExpNames, altExps, clearSizeFactors, clearSpikes, cpm, factorData, featureLoadings, int_colData, int_elementMetadata, int_metadata, isSpike, logcounts, normcounts, objectVersion, reducedDim, reducedDimNames, reducedDims, removeAltExps, sampleFactors, sizeFactorNames, spikeNames, splitAltExps, swapAltExp, tpm ExportMethods: weights, updateObject, tpm, spikeNames, sizeFactors, sizeFactorNames, show, sampleFactors, rowData, reducedDims, reducedDimNames, reducedDim, rbind, objectVersion, normcounts, logcounts, isSpike, int_metadata, int_elementMetadata, int_colData, featureLoadings, factorData, dimnames, dim, cpm, counts, colData, coerce, clearSpikes, clearSizeFactors, cbind, as.matrix, altExps, altExpNames, altExp, weights<-, tpm<-, sizeFactors<-, sampleFactors<-, reducedDims<-, reducedDimNames<-, reducedDim<-, normcounts<-, logcounts<-, isSpike<-, int_metadata<-, int_elementMetadata<-, int_colData<-, featureLoadings<-, factorData<-, dimnames<-, cpm<-, counts<-, altExps<-, altExpNames<-, altExp<-, [<-, [, $<-, $ ExportClasses: SingleCellExperiment, LinearEmbeddingMatrix Package: singleCellTK Exports: ComBatSCE, DownsampleCells, DownsampleDepth, MAST, MASTregression, MASTviolin, SCtkExperiment, alignSingleCellData, calcEffectSizes, convertGeneIDs, createSCE, distinctColors, enrichRSCE, filterSCData, generateSimulatedData, getBiomarker, getClusterInputData, getPCA, getTSNE, getUMAP, gsvaPlot, gsvaSCE, iterateSimulations, parseRsubreadLogs, plotBatchVariance, plotBiomarker, plotDiffEx, plotDimRed, plotPCA, plotTSNE, plotUMAP, saveBiomarkerRes, saveDiffExResults, scDiffEx, scDiffExANOVA, scDiffExDESeq2, scDiffExlimma, singleCellTK, subDiffEx, subDiffExANOVA, subDiffExttest, summarizeTable, thresholdGenes, visPlot ExportMethods: pcaVariances, pcaVariances<- ExportClasses: SCtkExperiment Package: SingleR Exports: BlueprintEncodeData, DatabaseImmuneCellExpressionData, HumanPrimaryCellAtlasData, ImmGenData, MonacoImmuneData, MouseRNAseqData, NovershternHematopoieticData, SingleR, aggregateReference, classifySingleR, getDeltaFromMedian, matchReferences, plotScoreDistribution, plotScoreHeatmap, pruneScores, trainSingleR Package: singscore Exports: generateNull, getPvals, multiScore, plotDispersion, plotNull, plotRankDensity, plotScoreLandscape, projectScoreLandscape, rankGenes, simpleScore Package: SISPA Exports: SISPA, callGSVA, callZSCORE, cptSamples, filterVars, freqplot, sortData, waterfallplot Package: sitePath Exports: SNPsites, addMSA, extractSite, extractTips, fixationSites, groupTips, lineagePath, multiFixationSites, plotSingleSite, setSiteNumbering, similarityMatrix, sneakPeek Package: sizepower Exports: sampleSize.randomized, sampleSize.matched, power.randomized, power.matched, power.multi Package: skewr Exports: getSNparams, panelPlots, getMethyLumiSet, preprocess, subsetProbes, getBarcodes Package: slalom Exports: addResultsToSingleCellExperiment, initSlalom, newSlalomModel, plotLoadings, plotRelevance, plotTerms, topTerms, trainSlalom, updateSlalom ExportClasses: Rcpp_SlalomModel Package: SLGI Exports: gi2Interactome, getInteraction, getSharedInteraction, hyperG, comemberIn, congruence, normInteraction, topInteraction, createSquareMatrix, byComplex, domainDist, getSharedDomains, sharedBy, getUniquePairs, getTestedPairs, seqMatcherAlign, getAlignStats, twoWayTable, modelSLGI, test2Interact, iSummary, withinComplex, sharedInt ExportMethods: plot, compare, show ExportClasses: siResult Package: slingshot Exports: SlingshotDataSet, getCurves, getLineages, newSlingshotDataSet, plot3d.SlingshotDataSet, plotGenePseudotime, slingAdjacency, slingClusterLabels, slingCurveWeights, slingCurves, slingLineages, slingParams, slingPseudotime, slingshot ExportMethods: slingshot, slingPseudotime, slingParams, slingLineages, slingCurves, slingCurveWeights, slingClusterLabels, slingAdjacency, show, reducedDims, reducedDim, predict, plotGenePseudotime, plot, newSlingshotDataSet, lines, getLineages, getCurves, SlingshotDataSet, [ ExportClasses: SlingshotDataSet Package: slinky Exports: Slinky ExportMethods: rzs, rownames, readGCTX, nrow, ncol, metadata, loadL1K, get_metadata, download, diffexp, controls, colnames, coerce, clueVehicle, clueInstances, clueCount, clue, closeAll ExportClasses: Slinky Package: SLqPCR Exports: geneStabM, geomMean, normPCR, relQuantPCR, selectHKgenes Package: SMAD Exports: CompPASS, HG 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: SMITE Exports: stoufferTest, scorePval, runGOseq, runSpinglass, runBioNet, plotModule, highScores, extractScores, extractModules, extractGOseq, searchGOseq, removeModification, plotDensityPval, plotCompareScores, normalizePval, makePvalueObject, makePvalueAnnotation, extractModSummary, extractModification, extractExpression, convertGeneIds, annotateModification, annotateExpression, addShadowText Package: SNAGEE Exports: qualStudy, qualSample, toSnageeFormat Package: snapCGH Exports: findBreakPoints, genomePlot, plotSegmentedGenome, processCGH, runBioHMM, runGLAD, runTilingArray, compareSegmentations, zoomChromosome, zoomGenome, read.clonesinfo, runHomHMM, mergeStates, runDNAcopy, simulateData, 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: SNPediaR Exports: extractGenotypeTags, extractSnpTags, extractTags, getCategoryElements, getPages Package: SNPhood Exports: analyzeSNPhood, annotationBins, annotationBins2, annotationDatasets, annotationReadGroups, annotationRegions, associateGenotypes, changeObjectIntegrityChecking, collectFiles, convertToAllelicFractions, deleteDatasets, deleteReadGroups, deleteRegions, enrichment, getDefaultParameterList, mergeReadGroups, nBins, nDatasets, nReadGroups, nRegions, parameters, plotAllelicBiasResults, plotAllelicBiasResultsOverview, plotAndCalculateCorrelationDatasets, plotAndCalculateWeakAndStrongGenotype, plotAndClusterMatrix, plotAndSummarizeAllelicBiasTest, plotBinCounts, plotClusterAverage, plotFDRResults, plotGenotypesPerCluster, plotGenotypesPerSNP, plotRegionCounts, renameBins, renameDatasets, renameReadGroups, renameRegions, results, testForAllelicBiases ExportMethods: parameters, enrichment, counts, annotation Package: SNPRelate Exports: .onAttach Package: snpStats Exports: can.impute, convert.snpMatrix, convert.snpMatrix.dir, filter.rules, Fst, glm.test.control, g2post, ibsCount, ibsDist, impute.snps, imputation.maf, imputation.r2, imputation.nsnp, ld, mean2g, misinherits, mvtests, plotUncertainty, pool, post2g, pp, qq.chisq, read.beagle, read.impute, read.long, read.mach, read.pedfile, read.plink, read.snps.long, random.snps, row.summary, col.summary, single.snp.tests, sm.compare, snp.cor, snp.imputation, snp.lhs.tests, snp.lhs.estimates, snp.post.multiply, snp.pre.multiply, snp.rhs.tests, snp.rhs.estimates, tdt.snp, test.allele.switch, write.plink, write.SnpMatrix, xxt ExportMethods: cbind, chi.squared, deg.freedom, effect.sign, is.na, names, pool2, p.value, rbind, show, summary, switch.alleles, plot, sample.size, effective.sample.size, [, [<-, coerce, initialize ExportClasses: SnpMatrix, XSnpMatrix, ImputationRules, SingleSnpTests, SingleSnpTestsScore, GlmTests, GlmEstimates Package: soGGi Exports: findconsensusRegions, groupByOverlaps, makeMotifScoreRle, normalise.ChIPprofile, normaliseQuantiles.ChIPprofile, orientBy, pwmToCoverage, regionPlot, summitPipeline ExportMethods: rbind, plotRegion, normaliseQuantiles, normalise, mean, log2, log, cbind, c, Ops, [[, $ ExportClasses: ChIPprofile Package: sojourner Exports: Dcoef, bootstrap, combineTrackll, compareFolder, compare_RT_CDF, createTrackll, densityMaskTracks, dispVariance, dispVariance_track, displacementCDF, dwellTime, exportTrackll, filterOnCell, filterTrack, fitCDF, fitNormDistr, fitRT, getCI, hmmTrackll, indexCell, linkSkippedFrames, maskTracks, mergeTracks, msd, msd_perc, msd_track, msd_track_vecdt, plotComponentTrackOverlay, plotIndividualTracks, plotLines, plotLinesTrackl, plotLocalizations_Density, plotMask, plotNucTrackOverlay, plotNucTrackOverlayTrackl, plotPoints, plotPointsTrackl, plotTrack, plotTrackFromIndex, plotTrackOverlay, plotTrackOverlay_Dcoef, sampleTracks, selComponentTracks, sojournerGUI, squareDisp, squareDispCpp, trackLength, trimTrack Package: SomaticSignatures Exports: readMutect, ucsc, ncbi, seqchar, mutationContext, mutationContextMutect, kmerFrequency, mutationDistance, plotRainfall, plotVariantAbundance, motifMatrix, identifySignatures, plotMutationSpectrum, plotObservedSpectrum, plotFittedSpectrum, plotSignatureMap, plotSignatures, plotSampleMap, plotSamples, gcContent, hsToplevel, hsAutosomes, hsAllosomes, hsLinear, normalizeMotifs, clusterSpectrum, nmfDecomposition, pcaDecomposition, nmfSignatures, pcaSignatures, assessNumberSignatures, plotNumberSignatures ExportMethods: show, signatures, samples, observed, fitted ExportClasses: MutationalSignatures Package: SpacePAC Exports: SpaceClust, make.3D.Sphere Package: Spaniel Exports: createSCE, createSeurat, markClusterCol, parseImage, removeSpots, runShinySpaniel, selectSpots, spanielPlot Package: sparseDOSSA Exports: sparseDOSSA Package: sparsenetgls Exports: assess_direct, convertbeta, glassonet2, lassoglmnet, path_result_for_roc, plot_roc, plotsngls, sparsenetgls Package: SparseSignatures Exports: as.alpha, as.alpha.in.range, as.beta, as.beta.in.range, as.loglik.progression, as.loglik.progression.in.range, as.mean.squared.error, as.starting.beta, as.starting.beta.in.range, evaluate.lambda.range, import.counts.data, nmf.LassoCV, nmf.LassoK, patient.plot, signatures.plot, starting.betas.estimation Package: SpatialCPie Exports: parseSpotFile, runCPie Package: SpeCond Exports: getDefaultParameter, createParameterMatrix, fitPrior, fitNoPriorWithExclusion, getSpecificResult, getSpecificOutliersStep1, SpeCond, getMatrixFromExpressionSet, getProfile, writeSpeCondResult, writeUniqueProfileSpecificResult, writeGeneResult, getFullHtmlSpeCondResult, getGeneHtmlPage Package: SpectralTAD Exports: SpectralTAD, SpectralTAD_Par Package: SPEM Exports: SPEM, row_optimize, s_diff Package: SPIA Exports: spia, plotP, combfunc, makeSPIAdata Package: SpidermiR Exports: SpidermiRanalyze_Community_detection, SpidermiRanalyze_Community_detection_bi, SpidermiRanalyze_Community_detection_net, SpidermiRanalyze_degree_centrality, SpidermiRanalyze_direct_net, SpidermiRanalyze_direct_subnetwork, SpidermiRanalyze_mirnanet_pharm, SpidermiRanalyze_subnetwork_neigh, SpidermiRdownload_miRNAextra_cir, SpidermiRdownload_miRNAprediction, SpidermiRdownload_miRNAvalidate, SpidermiRdownload_net, SpidermiRdownload_pharmacomir, SpidermiRprepare_NET, SpidermiRquery_disease, SpidermiRquery_networks_type, SpidermiRquery_spec_networks, SpidermiRquery_species, SpidermiRvisualize_3Dbarplot, SpidermiRvisualize_BI, SpidermiRvisualize_adj_matrix, SpidermiRvisualize_degree_dist, SpidermiRvisualize_direction, SpidermiRvisualize_mirnanet, SpidermiRvisualize_plot_target 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: splatter Exports: BASiCSEstimate, BASiCSSimulate, addGeneLengths, compareSCEs, diffSCEs, getParam, getParams, kersplatEstimate, kersplatSample, kersplatSetup, kersplatSimulate, listSims, lun2Estimate, lun2Simulate, lunEstimate, lunSimulate, makeCompPanel, makeDiffPanel, makeOverallPanel, mfaEstimate, mfaSimulate, newBASiCSParams, newKersplatParams, newLun2Params, newLunParams, newMFAParams, newPhenoParams, newSCDDParams, newSimpleParams, newSparseDCParams, newSplatParams, newZINBParams, phenoEstimate, phenoSimulate, scDDEstimate, scDDSimulate, setParam, setParams, simpleEstimate, simpleSimulate, sparseDCEstimate, sparseDCSimulate, splatEstimate, splatSimulate, splatSimulateGroups, splatSimulatePaths, splatSimulateSingle, summariseDiff, zinbEstimate, zinbSimulate ExportClasses: ZINBParams, SplatParams, SparseDCParams, SimpleParams, SCDDParams, PhenoParams, MFAParams, LunParams, Lun2Params, KersplatParams, BASiCSParams Package: SPLINTER Exports: addEnsemblAnnotation, annotateEvents, callPrimer3, checkPrimer, eventOutcomeCompare, eventOutcomeTranslate, eventPlot, extendROI, extractSpliceEvents, extractSpliceSites, findCompatibleEvents, findCompatibleExon, findTX, getPCRsizes, getRegionDNA, insertRegion, makeROI, makeUniqueIDs, plot_seqlogo, psiPlot, removeRegion, shapiroAcceptor, shapiroDensity, shapiroDonor, splitPCRhit Package: splots Exports: plotScreen Package: SPONGE Exports: sample_zero_mscor_cov, sample_zero_mscor_data, sponge, sponge_build_null_model, sponge_compute_p_values, sponge_edge_centralities, sponge_gene_miRNA_interaction_filter, sponge_network, sponge_node_centralities, sponge_plot_network, sponge_plot_network_centralities, sponge_plot_simulation_results, sponge_run_benchmark, sponge_subsampling Package: spotSegmentation Exports: spotseg, spotgrid, plotBlockImage Package: SQLDataFrame Exports: SQLDataFrame, coerce, connSQLDataFrame, makeSQLDataFrame, saveSQLDataFrame ExportMethods: union, tblData, tail, show, rbind, names, length, head, dimnames, dim, dbtable, dbnrows, dbkey, dbconcatKey, as.data.frame, ROWNAMES, dbkey<-, [[, [, $ ExportClasses: SQLDataFrame Package: SQUADD Exports: simResService ExportMethods: [, [<-, getFittedTable, plotCC, plotPredMap, plotSimMatrix ExportClasses: SquadSimResServiceImpl Package: sRACIPE Exports: sracipeCircuit<-, sracipeConfig<-, sracipeIC<-, sracipeParams<-, RacipeSE, densityPlot, sracipeCircuit, sracipeConfig, sracipeGenParamNames, sracipeGeneEx, sracipeGetTS, sracipeHeatmapSimilarity, sracipeIC, sracipeKnockDown, sracipeNormalize, sracipeOverExp, sracipeParams, sracipePlotCircuit, sracipePlotData, sracipePlotParamBifur, sracipeSimulate ExportMethods: sracipeKnockDown, sracipeGetTS, sracipeCircuit, annotation, annotation<- ExportClasses: RacipeSE Package: sRAP Exports: RNA.norm, RNA.qc, RNA.deg, RNA.bdfunc.fc, RNA.bdfunc.signal, RNA.prepare.input Package: SRGnet Exports: SRGnet Package: srnadiff Exports: plotRegions, readAnnotation, srnadiff, srnadiffDefaultParameters, srnadiffExample, srnadiffExp ExportMethods: show, sampleInfo, regions, parameters, normFactors, coverages, countMatrix, chromosomeSizes, bamFiles, annotReg, parameters<-, normFactors<-, annotReg<- ExportClasses: srnadiffExp Package: sscore Exports: computeAffxSFandSDT, computeSFandSDT, SScore, SScoreBatch Package: sscu Exports: akashi_test, genomic_gc3, op_corre_CodonW, op_corre_NCprime, op_highly, op_highly_stats, low_frequency_op, s_index Package: ssize Exports: delta, delta.plot, pow, power.plot, power.t.test.FDR, ssize, ssize.plot Package: SSPA Exports: dbitri, pbitri, pilotData, predictpower, qbitri, rbitri, sampleSize, simdat ExportMethods: plot Package: ssrch Exports: DocSet, ctxsearch, docs2kw, docs2recs, docset_searchapp, ds_can1009b, kw2docs, parseDoc, retrieve_doc, searchDocs ExportClasses: DocSet Package: ssviz ExportMethods: plotPP, plotDistro, plotFreq, plotRegion, readBam, pingpong, ntfreq, getCountMatrix ExportClasses: logicalORmissing Package: stageR Exports: adjustedAlphaLevel, getAdjustedPValues, getAlpha, getMethod, getPConfirmation, getPScreen, getResults, getSignificantGenes, getSignificantTx, getTx2gene, isAdjusted, isPScreenAdjusted, stageR, stageRTx, stageWiseAdjustment ExportMethods: stageWiseAdjustment, isPScreenAdjusted, isAdjusted, getTx2gene, getSignificantTx, getSignificantGenes, getResults, getPScreen, getPConfirmation, getMethod, getAlpha, getAdjustedPValues, adjustedAlphaLevel ExportClasses: stageRTx, stageR Package: STAN Exports: initBdHMM, data2Gviz, viterbi2Gviz, getAvgSignal, binarizeData, runningMean, getSizeFactors, viterbi2GRanges, initHMM, getLogLik, DirScore, DimNames, LogLik, StateNames, Transitions, InitProb, Emission, EmissionParams, HMM, HMMEmission, bdHMM, getViterbi, fitHMM, getPosterior, call_dpoilog, initBdClust, fitBdClust ExportClasses: bdHMM, HMMEmission, HMM Package: staRank Exports: RankSummary, aggregRank, dataFormatRSA, getRankmatrix, getStability, mwTest2samp, runRSA, uniqueRSARanking ExportMethods: summaryStats, stableSetSize, stabilityRanking, stabRank, rankCor, method, getSampleScores, baseRank, avrgRank, Pi ExportClasses: RankSummary Package: StarBioTrek Exports: ConvertedIDgenes, GE_matrix, GE_matrix_mean, GetData, GetPathData, GetPathNet, IPPI, SelectedSample, average, circleplot, dsscorecrtlk, eucdistcrtlk, getNETdata, listpathnet, pathnet, plotcrosstalk, stdv, svm_classification Package: Starr Exports: bpmapToProbeAnno, profileplot, correlate, correlationPlot, expressionByFeature, fill, fillNA, filterGenes, getFeature, getIntensities, getMeans, getProfiles, getProfilesByBase, getRatio, intersection, list2matrix, makeProbeAnno, mapFeatures, normalize.Probes, plotBoxes, plotDensity, plotGCbias, plotImage, plotMA, plotPosBias, plotProfiles, rankPercentile.normalize, read.gffAnno, readCelFile, RGlist2ExpresionSet, sameLength, singleclusterplot, substract, whichIn, windowxy, writeGFF, writePosFile, densityscatter, kde2dplot, plotScatter, plotRatioScatter, makeSplines, backgd.sd, cmarrt.ma, cmarrt.peak, declare.bound, ma.stat, plotcmarrt, rm.small.peak, sortbygenomic, remap, match_ac, heatmapplot, writeWIG Package: STATegRa Exports: STATegRaUsersGuide, bioDist, bioDistFeature, bioDistFeaturePlot, bioDistW, bioDistWPlot, bioDistclass, bioMap, combiningMappings, createOmicsExpressionSet, getInitialData, getLoadings, getMethodInfo, getPreprocessing, getScores, getVAF, holistOmics, modelSelection, omicsCompAnalysis, omicsNPC, plotRes, plotVAF Package: statTarget Exports: mdsPlot, predict_RF, pvimPlot, rForest, shiftCor, shiftCor_dQC, statAnalysis, statTargetGUI, transX 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: strandCheckR Exports: checkPairedEnd, filterDNA, getWinFromBamFile, intersectWithFeature, plotHist, plotWin Package: Streamer ExportMethods: lapply, sapply ExportClasses: Streamer, Stream, Producer, RawInput, Seq, FunctionProducer, ConnectionProducer, Consumer, RawToChar, Rev, Downsample, Reducer, FunctionConsumer, Team, ParallelParam, MulticoreParam, DAGTeam, DAGParam Package: STRINGdb Exports: STRINGdb, coeffOfvar, delColDf, downloadAbsentFile, downloadAbsentFileSTRING, get_STRING_species, multi_map_df, plot_ppi_enrichment_graph, ppi_enrichment, ppi_enrichment_full, ppie.compLambda, ppie.compLambdaL1L2, ppie.compPij, ppie.getNumEdgesBetween, renameColDf ExportClasses: STRINGdb Package: STROMA4 Exports: assign.properties Package: Structstrings Exports: dotbracket<-, DB, DBDF, DBDFL, DBS, DBSL, DOTBRACKET_ALPHABET, DOTBRACKET_CHAR_VALUES, DotBracketDataFrame, DotBracketDataFrameList, DotBracketString, DotBracketStringSet, DotBracketStringSetList, LoopIndexList, SDBDFL, STRUCTURE_CLOSE_CHR, STRUCTURE_NEUTRAL_CHR, STRUCTURE_OPEN_CHR, SplitDotBracketDataFrameList, StructuredRNAStringSet, convertAnnotation, dotbracket, getBasePairing, getDotBracket, getLoopIndices, readDotBracketStringSet, readStructuredRNAStringSet, saveDotBracketStringSet, writeDotBracketStringSet, writeStructuredXStringSet ExportMethods: getLoopIndices, getDotBracket, getBasePairing, encoding, dotbracket, convertAnnotation, alphabet, dotbracket<-, colnames<-, [<- ExportClasses: StructuredRNAStringSet, SplitDotBracketDataFrameList, LoopIndexList, DotBracketStringSetList, DotBracketStringSet, DotBracketString, DotBracketDataFrameList, DotBracketDataFrame, DotBracket, CompressedSplitDotBracketDataFrameList Package: StructuralVariantAnnotation Exports: breakendRanges, breakpointRanges, breakpointgr2bedpe, breakpointgr2pairs, countBreakpointOverlaps, findBreakpointOverlaps, isStructural, isSymbolic, pairs2breakpointgr, partner Package: SubCellBarCode Exports: applyThresholdCompartment, applyThresholdNeighborhood, calRowMean, calculateCoveredProtein, candidateRelocatedProteins, computeThresholdCompartment, computeThresholdNeighborhood, loadData, markerQualityControl, mergeCls, mergeProbability, plotBarcode, plotMultipleProtein, replacePrediction, sankeyPlot, sumProbability, svmClassification, tsneVisualization Package: subSeq Exports: combineSubsamples, generateSubsampledMatrix, getSeed, subsample Package: SummarizedBenchmark Exports: BDData<-, BDMethod<-, BDMethodList<-, groundTruths<-, performanceMetrics<-, BDData, BDMethod, BDMethodList, BenchDesign, SummarizedBenchmark, addMethod, addPerformanceMetric, availableMetrics, buildBench, compareBDData, compareBDMethod, compareBenchDesigns, dropMethod, estimateMetricsForAssay, estimatePerformanceMetrics, expandMethod, groundTruths, hashBDData, modifyMethod, performanceMetrics, plotMethodsOverlap, plotROC, printMethod, printMethods, tidyBDMethod, tidyUpMetrics, updateBench ExportMethods: tidyBDMethod, compareBenchDesigns, BDMethod, performanceMetrics<-, performanceMetrics, mcols<-, groundTruths<-, groundTruths, assayNames<-, BenchDesign, BDMethodList<-, BDMethodList, BDMethod<-, BDData<- ExportClasses: SummarizedBenchmark, BenchDesign, BDMethodList, BDMethod, BDData Package: SummarizedExperiment Exports: Assays, SummarizedExperiment, .DollarNames.SummarizedExperiment, .DollarNames.RangedSummarizedExperiment, makeSummarizedExperimentFromExpressionSet, makeSummarizedExperimentFromDataFrame, makeSummarizedExperimentFromLoom, naiveRangeMapper, probeRangeMapper, geneRangeMapper, readKallisto, readKallistoBootstrap, KALLISTO_ASSAYS, rowRanges<-, rowData, rowData<-, colData, colData<-, assayNames, assayNames<-, assays, assays<-, assay, assay<- ExportMethods: rowRanges<-, rowData, rowData<-, colData, colData<-, assayNames, assayNames<-, assays, assays<-, assay, assay<-, length, names, names<-, dim, dimnames, dimnames<-, [, [<-, [[, [[<-, $, $<-, as.data.frame, coerce, show, c, merge, Compare, cbind, rbind, duplicated, match, is.unsorted, order, rank, sort, start, start<-, end, end<-, width, width<-, strand, strand<-, updateObject, metadata<-, mcols, mcols<-, elementMetadata, elementMetadata<-, values, values<-, extractROWS, replaceROWS, subset, pcompare, ranges, ranges<-, shift, narrow, resize, flank, promoters, restrict, trim, isDisjoint, disjointBins, coverage, findOverlaps, precede, follow, nearest, distance, distanceToNearest, seqinfo, seqinfo<-, seqnames, seqnames<-, acbind, arbind, rowRanges, realize ExportClasses: Assays, SimpleAssays, ShallowData, ShallowSimpleListAssays, SummarizedExperiment, RangedSummarizedExperiment Package: supraHex Exports: sBMH, sCompReorder, sDistance, sDmat, sDmatCluster, sDmatMinima, sHexDist, sHexGrid, sHexGridVariant, sHexPolygon, sInitial, sMapOverlay, sNeighAny, sNeighDirect, sPipeline, sTopology, sTrainBatch, sTrainSeq, sTrainology, sWriteData, visColoralpha, visColorbar, visColormap, visCompReorder, visDmatCluster, visDmatHeatmap, visHeatmap, visHeatmapAdv, visHexAnimate, visHexBarplot, visHexComp, visHexGrid, visHexMapping, visHexMulComp, visHexPattern, visKernels, visTreeBSclust, visTreeBootstrap, visVp Package: Sushi Exports: addlegend, labelgenome, labelplot, maptocolors, maptolwd, opaque, plotBed, plotBedgraph, plotBedpe, plotGenes, plotHic, plotManhattan, SushiColors, zoombox, zoomsregion Package: sva Exports: ComBat, empirical.controls, f.pvalue, fstats, fsva, irwsva.build, num.sv, psva, qsva, read.degradation.matrix, ssva, sva, sva.check, sva_network, svaseq, twostepsva.build Package: SVAPLSseq Exports: prop.vars, pvs.adj, pvs.unadj, sig.features, surr, svplsSurr, svplsTest ExportMethods: surr, sig.features, pvs.unadj, pvs.adj, prop.vars ExportClasses: svplsTest, svplsSurr Package: SwathXtend Exports: buildSpectraLibPair, checkQuality, cleanLib, canonicalFormat, readLibFile, plotRTCor, plotRTResd, plotRIICor, plotAll, outputLib, applyttest, applyttestPep, medianNorm, mlr, mlrGroup, mlrrep, plotDensities, plotRelativeDensities, plotErrorBarsLines, coverage, cv, fdr.crit, swath.means, quantification.accuracy, getFdrBins, reliabilityCheckLibrary, reliabilityCheckSwath Package: swfdr Exports: calculateSwfdr, get_number_decimals, lm_pi0, lm_qvalue Package: SwimR Exports: createFrequencyMatrix, SwimR Package: switchBox Exports: SWAP.CalculateSignedScore, SWAP.KTSP.Train, SWAP.KTSP.Statistics, SWAP.KTSP.Classify, SWAP.Filter.Wilcoxon, KTSP.Train, KTSP.Classify, SWAP.GetKTSP.PredictionStats, SWAP.GetKTSP.Result, SWAP.GetKTSP.TrainTestResults, SWAP.PlotKTSP.TrainTestROC, SWAP.PlotKTSP.Genes, SWAP.PlotKTSP.GenePairScatter, SWAP.PlotKTSP.Votes, SWAP.PlotKTSP.GenePairBoxplot, SWAP.PlotKTSP.GenePairClassesBoxplot, SWAP.Train.KTSP, SWAP.Train.1TSP, SWAP.CalculateScores, SWAP.Kby.Measurement, SWAP.Kby.Ttest, SWAP.MakeTSPTable, SWAP.ScoreMatrixToVector, SWAP.ScoreVectorToMatrix, SWAP.MakeTrainTestData, SWAP.Calculate.SignedTSPScores, SWAP.Calculate.BasicTSPScores, SWAP.KTSP.CV, SWAP.KTSP.LOO, SWAP.GetKFoldIndices Package: switchde Exports: example_sigmoid, extract_pars, fit_nzi_model, fit_zi_model, switchde, switchplot Package: synapter Exports: Synapter, as.MSnSet.Synapter, createUniquePeptideDbRds, synergise, synergise1, synergise2, synergize, synergize1, synergize2, makeMaster, estimateMasterFdr, inspectPeptideScores, rescaleForTop3, synapterGuide, synapterTinyData ExportMethods: show, inputFiles, getLog, mergePeptides, modelRt, modelIntensity, findEMRTs, rescueEMRTs, searchGrid, fragmentMatching, fragmentMatchingPerformance, getGrid, getGridDetails, getBestGridValue, getBestGridParams, setBestGridParams, setPepScoreFdr, getPepScoreFdr, setProtFpr, getProtFpr, setIdentPpmError, getIdentPpmError, setQuantPpmError, getQuantPpmError, setPpmError, setLowessSpan, getLowessSpan, setRtNsd, getRtNsd, setImDiff, getImDiff, getPpmErrorQs, getRtQs, getPepNumbers, showFdrStats, getEMRTtable, setFragmentMatchingPpmTolerance, getFragmentMatchingPpmTolerance, performance, performance2, filterFragments, filterPeptideLength, filterQuantPepScore, filterIdentPepScore, filterIdentPpmError, filterQuantPpmError, filterIdentProtFpr, filterQuantProtFpr, filterUniqueDbPeptides, filterUniqueQuantDbPeptides, filterUniqueIdentDbPeptides, filterUniqueMatches, filterNonUniqueMatches, filterNonUniqueIdentMatches, plotPpmError, plotRtDiffs, plotRt, plotIntensity, plotPepScores, plotFdr, plotEMRTtable, plotGrid, plotFeatures, plotFragmentMatching, plotFragmentMatchingPerformance, plotCumulativeNumberOfFragments, writeMergedPeptides, writeMatchedEMRTs, writeIdentPeptides, writeQuantPeptides, bestComb, allComb, masterFdr, fileNames, plot, writeMasterPeptides, writeFragmentLibrary, getIdentificationFragments, getQuantitationSpectra, updateObject, requantify, synapterPlgsAgreement ExportClasses: MasterPeptides, MasterFdrResults Package: synergyfinder Exports: AddNoise, Bliss, CalculateSynergy, CorrectBaseLine, ExtractSingleDrug, FindModelType, FitDoseResponse, HSA, ImputeNA, Loewe, PlotDoseResponse, PlotSynergy, ReshapeData, ZIP Package: synlet Exports: bScore, madSelect, plateHeatmap, rankProdHits, rsaHits, scatterPlot, siRNAPlot, tTest, zFactor Package: SynMut ExportMethods: seq_random, input_seq, get_rscu, get_region, get_nu, get_freq, get_du, get_dna, get_cu, dinu_to, dinu_dist, codon_to, codon_random, codon_mimic, codon_dist ExportClasses: regioned_dna Package: systemPipeR Exports: readComp, writeTargetsout, writeTargetsRef, mergeBamByFactor, alignStats, getQsubargs, qsubRun, clusterRun, returnRPKM, runCommandline, systemArgs, symLink2bam, moduleload, modulelist, module, run_edgeR, run_DESeq2, filterDEGs, seeFastq, seeFastqPlot, GOHyperGAll, GOHyperGAll_Subset, GOHyperGAll_Simplify, GOCluster_Report, makeCATdb, goBarplot, overLapper, vennPlot, olBarplot, preprocessReads, filterVars, variantReport, combineVarReports, varSummary, countRangeset, runDiff, genFeatures, featuretypeCounts, plotfeaturetypeCounts, featureCoverage, plotfeatureCoverage, predORF, scaleRanges, loadWorkflow, loadWF, renderWF, subsetWF, output_update, targets.as.df, run_track, olRanges, createWF ExportMethods: targetsin, targetsout, targetsheader, modules, software, cores, other, reference, results, infile1, infile2, outfile1, SampleName, sysargs, outpaths, show, names, length, [, catmap, catlist, idconv, setlist, intersectmatrix, complexitylevels, vennlist, intersectlist, as.list, [[, [[<-, $, clt, cmdlist, cwlfiles, input, inputvars, output, SYSargs2list, targets, wf, yamlinput, SYSargs2Pipe_ls, WF_steps, track, summaryWF ExportClasses: SYSargs, catDB, VENNset, INTERSECTset, SYSargs2, SYSargs2Pipe Package: target Exports: associated_peaks, direct_targets, find_distance, merge_ranges, plot_predictions, rank_product, score_peaks, score_regions, target_app, test_predictions Package: TargetScore Exports: bsxfun.se, dot.ext, getTargetScores, initialization, logmvgamma, logsumexp, sort_components, targetScore, vbgmm, vbound, vexp, vmax Package: TargetSearch Exports: checkRimLim, FAMEoutliers, FindPeaks, FindAllPeaks, medianRILib, Profile, sampleRI, ImportLibrary, ImportLibrary.tab, ImportLibrary.msp, ImportSamples, ImportSamplesFromDir, ImportFameSettings, NetCDFPeakFinding, peakCDFextraction, peakFind, plotFAME, plotRIdev, plotAllRIdev, plotPeakSimple, plotPeak, plotSpectra, plotPeakRI, plotAllSpectra, quantMatrix, ProfileCleanUp, RIcorrect, rt2ri, ri2rt, Write.Results, writeMSP, baseline, baselineCorrection, baselineCorrectionQuant, fixRIcorrection, TargetSearchGUI, writeLibText, bin2text, text2bin, riMatrix, fixRI, ncdf4_convert, ncdf4_convert_from_path, ncdf4_data_extract 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<-, profileInfo, profileInfo<-, profileInt, profileInt<-, profileRI, profileRI<-, profileRT, profileRT<-, fileFormat, fileFormat<-, show, tsUpdate, ncdf4Convert ExportClasses: tsLib, tsRim, tsSample, tsMSdata, tsProfile Package: TCGAbiolinks Exports: GDCdownload, GDCprepare, GDCprepare_clinic, GDCquery, GDCquery_ATAC_seq, GDCquery_Maf, GDCquery_clinic, PanCancerAtlas_subtypes, TCGAVisualize_volcano, TCGA_MolecularSubtype, TCGAanalyze_Clustering, TCGAanalyze_DEA, TCGAanalyze_DEA_Affy, TCGAanalyze_DMR, TCGAanalyze_EAcomplete, TCGAanalyze_Filtering, TCGAanalyze_LevelTab, TCGAanalyze_Normalization, TCGAanalyze_Pathview, TCGAanalyze_Preprocessing, TCGAanalyze_Stemness, TCGAanalyze_SurvivalKM, TCGAanalyze_analyseGRN, TCGAanalyze_networkInference, TCGAanalyze_survival, TCGAbatch_Correction, TCGAprepare_Affy, TCGAquery_MatchedCoupledSampleTypes, TCGAquery_SampleTypes, TCGAquery_recount2, TCGAquery_subtype, TCGAtumor_purity, TCGAvisualize_BarPlot, TCGAvisualize_EAbarplot, TCGAvisualize_Heatmap, TCGAvisualize_PCA, TCGAvisualize_SurvivalCoxNET, TCGAvisualize_meanMethylation, TCGAvisualize_oncoprint, TCGAvisualize_starburst, UseRaw_afterFilter, colDataPrepare, gaiaCNVplot, get.GRCh.bioMart, getAdjacencyBiogrid, getDataCategorySummary, getGDCInfo, getGDCprojects, getGistic, getManifest, getResults, getSampleFilesSummary, get_IDs, isServeOK, matchedMetExp Package: TCGAbiolinksGUI Exports: TCGAbiolinksGUI Package: TCGAutils Exports: CpGtoRanges, TCGAbarcode, TCGAbiospec, TCGAprimaryTumors, TCGAsampleSelect, UUIDtoBarcode, UUIDtoUUID, barcodeToUUID, extractBuild, filenameToBarcode, findGRangesCols, generateMap, getClinicalNames, getFileName, getSubtypeMap, imputeAssay, makeGRangesListFromCopyNumber, makeGRangesListFromExonFiles, makeSummarizedExperimentFromGISTIC, mergeColData, mirToRanges, oncoPrintTCGA, qreduceTCGA, sampleTables, simplifyTCGA, splitAssays, symbolsToRanges, translateBuild, trimColData, uniformBuilds Package: TCseq Exports: DBanalysis, DBresult, DBresult.cluster, TCA, TCAFromSummarizedExperiment, clustCenters, clustCluster, clustData, clustMembership, clustResults, countReads, genomicFeature, peakreference, tcTable, timeclust, timeclustplot, timecourseTable ExportMethods: tcTable, design, counts, clustResults, clustMembership, clustData, clustCluster, clustCenters, counts<- ExportClasses: clust, TCA Package: TDARACNE Exports: TDARACNEdataPublished, TDARACNE Package: tenXplore Exports: tenXplore Package: TEQC Exports: chrom.barplot, coverage.correlation, coverage.density, coverage.hist, coverage.GC, coverage.plot, coverage.target, coverage.targetlength.plot, coverage.uniformity, covered.k, duplicates.barplot, fraction.reads.target, fraction.target, get.baits, get.reads, get.targets, insert.size.hist, make.wigfiles, multiTEQCreport, reads2pairs, readsPerTarget, TEQCreport Package: ternarynet Exports: tnetfit, tnetpost, ternaryFit, ternaryFitParameters, ternaryPost, graphPosterior, attractorSummary, plotTraces, plotFit, plotPost, predictAttractor, simulateSteadyState ExportMethods: scores, degreeObjs, graphObjs, tableObjs, scores<-, degreeObjs<-, graphObjs<-, tableObjs<-, perturbationType, scoreType, backupStage, maxStage, maxTransition, epsilon, beta0, chi0, delta, ne, m0, maxDegree, pAddParent, pExchangeParent, neighborDegree, pNeighborhood, rho, edgePenalty, show, perturbationType<-, scoreType<-, backupStage<-, maxStage<-, maxTransition<-, epsilon<-, beta0<-, chi0<-, delta<-, ne<-, m0<-, maxDegree<-, pAddParent<-, pExchangeParent<-, neighborDegree<-, pNeighborhood<-, rho<-, edgePenalty<-, dim, perturbationObj, steadyStateObj, geneNames, experimentNames, degreeObjMin, graphObjMin, tableObjMin, newScore, minScore, finalTemperature, traces, stageCount, xSeed, inputParams, perturbationObj<-, steadyStateObj<-, geneNames<-, experimentNames<-, degreeObjMin<-, graphObjMin<-, tableObjMin<-, newScore<-, minScore<-, finalTemperature<-, traces<-, stageCount<-, xSeed<-, inputParams<- ExportClasses: ternaryFitParameters, ternaryFit, ternaryPost Package: TFARM Exports: IComp, IPCA, distribViz, heatI, items, itemset, presAbs, rulesGen, rulesTF, rulesTF0, search_rule Package: TFBSTools Exports: PFMatrix, PFMatrixList, ICMatrix, ICMatrixList, PWMatrix, PWMatrixList, MotifSet, SitePairSetList, SitePairSet, SiteSet, SiteSetList, TFFMFirst, TFFMDetail, shannon.entropy, IUPAC2Matrix, sampleRanges, parseMEMEOutput, readXMLTFFM, storeMatrix, getMatrixSet, getMatrixByID, getMatrixByName, deleteMatrixHavingID, initializeJASPARDB, makeFlatFileDir, readJASPARMatrix, ID, name, matrixClass, Matrix, Matrix<-, bg, tags, matrixType, XMatrixList, toPWM, searchSeq, searchAln, searchPairBSgenome, PWMSimilarity, toICM, seqLogo, totalIC, writeGFF3, writeGFF2, relScore, views, pvalues, toGRangesList, calConservation, PFMSimilarity, permuteMatrix, dmmEM, rPWMDmm, runMEME, sitesSeq, getEmissionProb, getPosProb ExportMethods: length, ncol, dim, reverseComplement, showAsCell, start, end, as.matrix, as.data.frame, colSums, rowSums, consensusMatrix ExportClasses: PFMatrix, PWMatrix, ICMatrix, PFMatrixList, PWMatrixList, ICMatrixList, SiteSet, SiteSetList, SitePairSet, SitePairSetList, MotifSet Package: TFEA.ChIP Exports: GR2tfbs_db, GSEA_EnrichmentScore, GSEA_run, GeneID2entrez, Select_genes, contingency_matrix, getCMstats, get_chip_index, makeTFBSmatrix, plot_CM, plot_ES, plot_RES, preprocessInputData, rankTFs, set_user_data, txt2GR Package: TFHAZ Exports: accumulation, dense_zones, n_zones_PCA, plot_accumulation, plot_n_zones, w_analysis, high_accumulation_zones Package: TFutils Exports: HGNCmap, TFCatalog, TFtargs, URL_s3_tf, anchor_pmids, browse_lambert_gwaslinks, browse_lambert_main, defaultCircosParms, directHitsInCISBP, fimo_granges, genemodForGviz, genemodelDF, get_rslocs_38, grabTab, importFIMO_local_split, retrieve_lambert_main, tffamCirc.plot, tffamCirc.prep, topTraitsOfTargets ExportMethods: show, importFIMO ExportClasses: TFCatalog 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: timescape Exports: checkAlpha, checkClonalPrev, checkCloneColours, checkGtypePositioning, checkMinDims, checkPerts, checkRequiredInputs, checkTreeEdges, getMutationsData, processUserData, renderTimescape, replaceSpaces, timescape, timescapeOutput Package: TimeSeriesExperiment Exports: %>%, assayCollapsed<-, colDataCollapsed<-, groups<-, replicates<-, timeSeries<-, timepoints<-, TimeSeriesExperiment, addLags, assayCollapsed, assignClusterStatic, clusterAssignment, clusterData, clusterMap, clusterTimeSeries, colDataCollapsed, collapseReplicates, dataToTimeSeries, differentialExpression, dimensionReduction, filterFeatures, groups, makeTimeSeries, makeTimeSeriesExperimentFromExpressionSet, makeTimeSeriesExperimentFromSummarizedExperiment, meltMatrix, normalizeData, pathwayEnrichment, plotEnrichment, plotHeatmap, plotSamplePCA, plotTimeSeries, plotTimeSeriesClusters, plotTimeSeriesPCA, replicates, runPCA, timeSeries, timepointDE, timepoints, trajectoryDE, varianceStabilization ExportMethods: timepoints, timeSeries, show, replicates, groups, dimensionReduction, differentialExpression, colDataCollapsed, clusterMap, clusterAssignment, assayCollapsed, timepoints<-, timeSeries<-, rownames<-, rowData<-, replicates<-, groups<-, colnames<-, colDataCollapsed<-, colData<-, assayCollapsed<- ExportClasses: TimeSeriesExperiment Package: TIN Exports: firmaAnalysis, readGeneSummaries, aberrantExonUsage, probesetPermutations, correlation, clusterPlot, scatterPlot, correlationPlot, posNegCorrPlot, geneSetCorrelation Package: TissueEnrich Exports: teEnrichment, teEnrichmentCustom, teGeneRetrieval Package: TitanCNA Exports: loadAlleleCounts, loadDefaultParameters, filterData, getPositionOverlap, wigToRangedData, wigToGRanges, outputTitanResults, outputModelParameters, correctReadDepth, runEMclonalCN, viterbiClonalCN, computeSDbwIndex, plotAllelicRatio, plotClonalFrequency, plotCNlogRByChr, plotIdiogram.hg38, plotSubcloneProfiles, outputTitanSegments, setGenomeStyle, plotSegmentMedians, loadHaplotypeAlleleCounts, plotHaplotypeFraction, getHaplotypesFromVCF, loadBXcountsFromBEDDir, correctIntegerCN 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: TMixClust Exports: TMixClust, analyse_stability, generate_TMixClust_report, get_time_series_df, get_time_series_df_bio, plot_silhouette, plot_time_series_df Package: TNBC.CMS Exports: computeDS, computeGES, performGSVA, plotHR, plotKM, predictCMS Package: TnT Exports: tooltip<-, trackData<-, trackSpec<-, tracklist<-, AreaTrack, BlockTrack, FeatureTrack, GeneTrackFromTxDb, GroupFeatureTrack, LineTrack, PinTrack, TnTBoard, TnTGenome, TnTOutput, TxTrackFromGRanges, TxTrackFromTxDb, VlineTrack, mapcol, renderTnT, saveTnT, strandlabel, tooltip, trackData, trackSpec, trackWidget, tracklist ExportMethods: merge Package: TOAST Exports: assignCellType, csDeconv, csTest, DEVarSelect, findRefinx, fitModel, makeDesign Package: tofsims Exports: analysis<-, analysisName<-, calibPoints<-, calibration<-, instrument<-, nz<-, peakIDs<-, peakMzs<-, xy<-, MAF, MNF, MassImage, MassSpectra, PCAnalysis, PeakList, addFixedWidth, addPeaks, analysis, analysisName, binning, bwApply, calibPointNew, calibPoints, calibration, changePeakWidth, findPeakWidth, getTOFs, image, imageMatrix, instrument, nComp, nPeaks, nnMNF, nz, opaMCR, overlayPlot, pcaLoadings, pcaScores, peakIDs, peakMzs, peakPick, peakWidths, peaks2Spectra, plot, points, poissonScaling, prComp, prinComp, recalibrate, reduceSpectrumResolution, removePeaks, scale, smoothScatter, smootherGolay, smootherSpline, subset, unitMassPeaks, xy, xySpec ExportMethods: poissonScaling ExportClasses: PrinComp, PrComp, PCA, MCR Package: ToPASeq Exports: CePa, DEGraph, PRS_wrapper, PWEA, SPIA, TAPPA, TopologyGSA, clipper, convertIdentifiersByVector, degtable, prs, prsWeights, res, topo.sig Package: topconfects Exports: confects_plot, confects_plot_me, deseq2_confects, edger_confects, limma_confects, nest_confects, normal_confects, rank_rank_plot Package: TPP Exports: analyzeTPPCCR, analyzeTPPTR, analyze2DTPP, tppDefaultTheme, tppExport, tppQCPlotsCorrelateExperiments, tppccrCurveFit, tppccrImport, tppccrNormalize, tppccrNormalizeToReference, tppccrPlotCurves, tppccrResultTable, tppccrTransform, tpptrAnalyzeMeltingCurves, tpptrCurveFit, tpptrDefaultNormReqs, tpptrImport, tpptrNormalize, tpptrSplineFitAndTest, tpptrFitSplines, tpptrPlotSplines, tpptrFTest, tpptrTidyUpESets, tpp2dAddAdditionalInfo, tpp2dEvalConfigTable, tpp2dCalcFractAbundance, tpp2dComputeFoldChanges, tpp2dCreateCCRConfigFile, tpp2dCreateDRplots, tpp2dCreateReport, tpp2dCreateTPPTRreference, tpp2dCurveFit, tpp2dExport, tpp2dExportPlots, tpp2dImport, tpp2dMerge2dRef, tpp2dNormalize, tpp2dPlotCCRAllCurves, tpp2dPlotCCRGoodCurves, tpp2dPlotCCRSingleCurves, tpp2dPlotQCpEC50, tpp2dPlotQChist, tpp2dRemoveZeroSias, tpp2dSplineFitAndTest, tpp2dTRReferenceObject Package: TPP2D Exports: TPP_importCheckConfigTable, annotateDataList, bootstrapNull, competeModels, computeFdr, computeFstat, configWide2Long, filterOutContaminants, findHits, fitAndEvalDataset, fitH0Model, fitH1Model, gg_qq, import2dDataset, import2dMain, plot2dTppFit, plot2dTppProfile, plot2dTppRelProfile, recomputeSignalFromRatios, renameColumns Package: tracktables Exports: MakeIGVSampleMetadata, MakeIGVSession, MakeIGVSessionXML, igvParam, makebedtable, maketracktable Package: trackViewer Exports: GRoperator, addArrowMark, addGuideLine, browseTracks, browseTracksOutput, coverageGR, dandelion.plot, geneModelFromTxdb, geneTrack, getCurTrackViewport, getLocation, gieStain, ideogramPlot, importBam, importData, importScore, loadIdeogram, lolliplot, optimizeStyle, parse2GRanges, parseWIG, plotGInteractions, plotGRanges, renderbrowseTracks, trackList, trackViewerStyle, viewGene, viewTracks ExportMethods: show, setTrackYaxisParam, setTrackXscaleParam, setTrackViewerStyleParam, setTrackStyleParam, $<-, $ ExportClasses: yaxisStyle, xscale, trackViewerStyle, trackStyle, trackList, track, pos Package: tradeSeq Exports: associationTest, clusterExpressionPatterns, diffEndTest, earlyDETest, evaluateK, fitGAM, getSmootherPvalues, getSmootherTestStats, patternTest, plotGeneCount, plotSmoothers, startVsEndTest ExportMethods: startVsEndTest, plotSmoothers, patternTest, fitGAM, evaluateK, earlyDETest, diffEndTest, clusterExpressionPatterns, associationTest Package: transcriptogramer Exports: radius<-, DE, Terms, clusterEnrichment, clusterVisualization, connectivityProperties, differentiallyExpressed, enrichmentPlot, orderingProperties, radius, transcriptogramPreprocess, transcriptogramStep1, transcriptogramStep2 ExportClasses: Transcriptogram Package: transcriptR Exports: addFeature, annotateTranscripts, breakTranscriptsByPeaks, constructCDS, constructTDS, detectTranscripts, estimateBackground, estimateGapDistance, exportCoverage, getConfusionMatrix, getGenomicAnnot, getPeaks, getPredictorSignificance, getProbTreshold, getQuadProb, getTestedGapDistances, getTranscripts, peaksToBed, plotErrorRate, plotFeatures, plotGenomicAnnot, plotROC, predictStrand, predictTssOverlap, transcriptsToBed ExportMethods: show ExportClasses: TranscriptionDataSet, ChipDataSet Package: transite Exports: calculateKmerEnrichment, calculateKmerScores, calculateLocalConsistency, calculateMotifEnrichment, calculateTranscriptMC, checkKmers, computeKmerEnrichment, createKmerMotif, createMatrixMotif, drawVolcanoPlot, empiricalEnrichmentMeanCDF, generateIUPACByKmers, generateIUPACByMatrix, generateKmers, generateKmersFromIUPAC, generatePermutedEnrichments, geometricMean, getMotifById, getMotifByRBP, getMotifs, getPPM, initIUPAClookupTable, motifsMetaInfo, pCombine, permTestGeometricMean, runKmerSPMA, runKmerTSMA, runMatrixSPMA, runMatrixTSMA, scoreSequences, scoreSpectrum, scoreTranscripts, setMotifs, spectrumClassifier, subdivideData ExportMethods: spectrumSlope, spectrumResiduals, spectrumFStatisticPValue, spectrumFStatistic, spectrumDegree, spectrumConsistencyScorePValue, spectrumConsistencyScoreN, spectrumConsistencyScore, spectrumAdjRSquared, plot, motifType, motifSpecies, motifSource, motifRbps, motifMatrix, motifLength, motifId, motifIUPAC, motifHexamers, motifHeptamers ExportClasses: SpectrumScore, RBPMotif Package: tRanslatome Exports: newTranslatomeDataset, computeDEGs, getExprMatrix, getConditionA, getConditionB, getConditionC, getConditionD, getDataType, getConditionLabels, getLevelLabels, getDEGs, Histogram, Scatterplot, MAplot, SDplot, CVplot, GOEnrichment, RegulatoryEnrichment, DEGs.table, getDEGsMethod, significance.threshold, FC.threshold, label.level.DEGs, label.condition, Radar, Heatmap, enriched.table, label.level.enriched, GOComparison, IdentityPlot, SimilarityPlot, identity.matrix, similarity.matrix, average.similarity.scores Package: TransView Exports: plotTV, parseReads, rmTV, annotatePeaks, gtf2gr, macs2gr, peak2tss, meltPeak ExportMethods: show, sliceN, slice1, sliceNT, slice1T, tvStats, plotTVData, histogram, ex_name, origin, spliced, paired, readthrough_pairs, filtered, strands, nreads, gcoverage, maxScore, lowqual, paired_reads, proper_pairs, collapsed, compression, chromosomes, filtered_reads, pos, neg, lcoverage, lmaxScore, fmapmass, env, data_pointer, spliced<-, ex_name<-, size, parameters, cluster_order, clusters, summaryTV, lsize, gsize ExportClasses: DensityContainer Package: traseR Exports: traseR, querySNP, queryGene, queryKeyword, plotSNP, plotGene, plotInterval, plotContext, plotPvalue, print.traseR Package: treeio Exports: %>%, MRCA, Nnode, Nnode2, Ntip, ancestor, as.phylo, as.treedata, as_tibble, child, data_frame, drop.tip, full_join, get.data, get.fields, get.placements, get.tree, get.treetext, getNodeNum, is.ggtree, is.rooted, isTip, label_branch_paml, mask, merge_tree, nodeid, nodelab, offspring, parent, raxml2nwk, read.astral, read.beast, read.codeml, read.codeml_mlc, read.fasta, read.hyphy, read.hyphy.seq, read.iqtree, read.jplace, read.jtree, read.mega, read.mega_tabular, read.mrbayes, read.newick, read.nexus, read.nhx, read.paml_rst, read.phylip, read.phylip.seq, read.phylip.tree, read.phyloT, read.r8s, read.raxml, read.tree, rename_taxa, rescale_tree, root, rootnode, rtree, tree_subset, treedata, write.beast, write.jplace, write.jtree, write.nexus, write.tree ExportMethods: get.treetext, drop.tip ExportClasses: jplace Package: TreeSummarizedExperiment Exports: LinkDataFrame, TreeSummarizedExperiment, aggValue, colLinks, colTree, countLeaf, countNode, distNode, findAncestor, findOS, findSibling, isLeaf, matTree, printNode, pruneTree, rowLinks, rowTree, shareNode, signalNode, toTree, trackNode, transNode ExportMethods: rowTree, rowLinks, colTree, colLinks, [ ExportClasses: TreeSummarizedExperiment, LinkDataFrame Package: trena Exports: BayesSpikeSolver, CandidateFilter, EnsembleSolver, FootprintFilter, FootprintFinder, GeneOntologyFilter, HumanDHSFilter, LassoPVSolver, LassoSolver, MotifMatcher, PCAMax, PearsonSolver, RandomForestSolver, RidgeSolver, Solver, SpearmanSolver, SqrtLassoSolver, Trena, VarianceFilter, XGBoostSolver, getAvailableSolvers, getCandidates, parseChromLocString, parseDatabaseUri, run ExportMethods: show, run, rescalePredictorWeights, normalizeModel, getTarget, getSolverNames, getSequence, getRegulatoryTableColumnNames, getRegulatoryRegions, getRegulatoryChromosomalRegions, getRegulators, getProximalPromoter, getPromoterRegionsAllGenes, getPfms, getGtfMoleculeTypes, getGtfGeneBioTypes, getGenePromoterRegion, getGeneModelTableColumnNames, getFootprintsInRegion, getFootprintsForGene, getEncodeRegulatoryTableNames, getCoverage, getChromLoc, getCandidates, getAssayData, findMatchesByChromosomalRegion, createGeneModelFromTfList, createGeneModelFromRegulatoryRegions, closeDatabaseConnections, assessSnp, addStatsSimple, addStats Package: Trendy Exports: breakpointDist, breakpointFit, extractPattern, fitSegBIC, formatFunc, formatResults, getCounts, plotFeature, results, topTrendy, trendHeatmap, trendy, trendyShiny Package: triform Exports: preprocess, triform Package: trigger Exports: trigger.build ExportMethods: trigger.link, trigger.mlink, trigger.eigenR2, trigger.loclink, trigger.net, trigger.netPlot2ps, trigger.export2cross, trigger.trait, plot ExportClasses: trigger Package: triplex Exports: triplex.search, triplex.diagram, triplex.3D, triplex.alignment, triplex.score.table, triplex.group.table ExportMethods: show, score, pvalue, ins, type, lstart, lwidth, lend, strand, as.character, toString ExportClasses: TriplexViews Package: tRNA Exports: gettRNABasePairing, gettRNAFeaturePlots, gettRNALoopIDs, gettRNASummary, gettRNAstructureGRanges, gettRNAstructureSeqs, hasAcceptorStem, hasAnticodonLoop, hasAnticodonStem, hasDStem, hasDloop, hasTStem, hasTloop, hasVariableLoop, istRNAGRanges ExportMethods: istRNAGRanges, hasVariableLoop, hasTloop, hasTStem, hasDloop, hasDStem, hasAnticodonStem, hasAnticodonLoop, hasAcceptorStem, gettRNAstructureSeqs, gettRNAstructureGRanges, gettRNASummary, gettRNALoopIDs, gettRNAFeaturePlots, gettRNABasePairing Package: tRNAdbImport Exports: TRNA_DB_URL, TRNA_DB_URL_MT, import.mttRNAdb, import.mttRNAdb.id, import.tRNAdb, import.tRNAdb.blast, import.tRNAdb.id, istRNAdbGRanges, open_mtdbID, open_tdbID, tRNAdb2GFF ExportMethods: istRNAdbGRanges Package: tRNAscanImport Exports: get.tRNAprecursor, import.tRNAscanAsGRanges, istRNAscanGRanges, tRNAscan2GFF, tRNAscanID ExportMethods: istRNAscanGRanges Package: TRONCO Exports: AND, OR, TCGA.map.clinical.data, TCGA.multiple.samples, TCGA.remove.multiple.samples, TCGA.shorten.barcodes, XOR, annotate.description, annotate.stages, as.adj.matrix, as.alterations, as.bootstrap.scores, as.colors, as.conditional.probs, as.confidence, as.description, as.events, as.events.in.patterns, as.events.in.sample, as.gene, as.genes, as.genes.in.patterns, as.genotypes, as.hypotheses, as.joint.probs, as.kfold.eloss, as.kfold.posterr, as.kfold.prederr, as.marginal.probs, as.models, as.parameters, as.pathway, as.patterns, as.samples, as.selective.advantage.relations, as.stages, as.types, as.types.in.patterns, cbio.query, change.color, consolidate.data, delete.event, delete.gene, delete.hypothesis, delete.model, delete.pattern, delete.samples, delete.type, duplicates, ebind, enforce.numeric, enforce.string, events.selection, export.graphml, export.mutex, export.nbs.input, extract.MAF.HuGO.Entrez.map, genes.table.report, has.duplicates, has.model, has.stages, hypothesis.add, hypothesis.add.group, hypothesis.add.homologous, import.GISTIC, import.MAF, import.genotypes, import.model, import.mutex.groups, intersect.datasets, is.compliant, join.events, join.types, keysToNames, nameToKey, nevents, ngenes, nhypotheses, npatterns, nsamples, ntypes, oncoprint, oncoprint.cbio, order.frequency, pathway.visualization, pheatmap, rank.recurrents, rename.gene, rename.type, samples.selection, sbind, ssplit, trim, tronco.bootstrap, tronco.caprese, tronco.capri, tronco.chowliu, tronco.edmonds, tronco.gabow, tronco.kfold.eloss, tronco.kfold.posterr, tronco.kfold.prederr, tronco.pattern.plot, tronco.plot, tronco.prim, view, which.samples Package: TSCAN Exports: TSCANorder, TSCANui, difftest, exprmclust, orderscore, plotmclust, preprocess, singlegeneplot Package: tspair Exports: ts.pair, tspcalc, tspsig, tspplot Package: TSRchitect Exports: TSRchitectUsersGuide, addAnnotationToTSR, addTagCountsToTSR, bedToTSS, createSummarizedExperiment, detTSR, determineTSR, getBamDataFirstRead, getBamDataLastRead, getFileNames, getTSRdata, getTSScountData, getTSStagData, getTitle, gsq2bed, importAnnotationExternal, importAnnotationHub, inputToTSS, loadTSSobj, makeGRangesFromTSR, mergeSampleData, processTSS, tsrCluster, tssObject, writeTSR, writeTSS Package: TTMap Exports: generate_correlation, generate_euclidean, generate_mismatch_distance, generate_p_val_correlation, generate_single_cell_complete_mismatch, generate_single_cell_mismatch_with_parameter, control_adjustment, hyperrectangle_deviation_assessment, ttmap, ttmap_sgn_genes, write_pcl, read_pcl, calcul_e, calcul_e_single, make_matrices Package: TurboNorm Exports: pspline, normalize.pspline, normalize.AffyBatch.pspline, turbotrend, panel.pspline Package: TVTB Exports: tSVE, TVTBparam, Genotypes, VcfFixedRules, VcfInfoRules, VcfVepRules, VcfFilterRules ExportMethods: type, mcols, c, eval, evalSeparately, subsetByFilter, active, active<-, metadata, metadata<-, colData, colData<-, readVcf, ScanVcfParam, header, header<-, geno, fixed, info, info<-, append, autodetectGenotypes, countGenos, addCountGenos, addFrequencies, addOverallFrequencies, addPhenoLevelFrequencies, vepInPhenoLevel, variantsInSamples, dropInfo, plotInfo, pairsInfo, genos, genos<-, ranges, ranges<-, aaf, aaf<-, maf, maf<-, ref, ref<-, het, het<-, alt, alt<-, carrier, vep, vep<-, bp, bp<-, suffix, svp, svp<- ExportClasses: TVTBparam, Genotypes, VcfFixedRules, VcfInfoRules, VcfVepRules, VcfFilterRules Package: tweeDEseq Exports: compareCountDist, testPoissonTweedie, mlePoissonTweedie, dPT, rPT, testShapePT, getParam, normalizeCounts, filterCounts, tweeDE, gofTest, qqchisq, MAplot, Vplot, glmPT, tweeDEglm, exactTestPT, tweeDExact Package: twoddpcr Exports: plateClassification<-, plateClassificationMethod<-, wellClassification<-, wellClassificationMethod<-, amplitudes, basicsSummary, castSummary, classCov, classMeans, classStats, clusterCentres, combinedCentres, commonClassificationMethod, copiesSummary, ddpcr, ddpcrPlate, ddpcrWell, dropletPlot, exportTable, exportZip, extractPlateName, extractWellNames, facetPlot, flatPlot, fullCopiesSummary, fullCountsSummary, ggplot.plate, ggplot.well, gridClassify, heatPlot, kmeansClassify, knnClassify, mahalanobisRain, mutantCopiesSummary, numDroplets, parseClusterCounts, plateClassification, plateClassificationMethod, plateSummary, positiveCounts, readCSVDataFrame, relabelClasses, removeDropletClasses, renormalisePlate, sdRain, setChannelNames, setDropletVolume, shinyVis, shinyVisApp, shinyVisServer, shinyVisUI, sortDataFrame, sortWells, thresholdClassify, wellClassification, wellClassificationMethod, whiteTheme, wildTypeCopiesSummary ExportMethods: wellClassificationMethod, wellClassification, thresholdClassify, setChannelNames, sdRain, removeDropletClasses, plateSummary, plateClassificationMethod, plateClassification, numDroplets, mahalanobisRain, knnClassify, kmeansClassify, isEmpty, heatPlot, gridClassify, ggplot.well, ggplot.plate, flatPlot, facetPlot, exportZip, exportTable, elementType, dropletPlot, ddpcrWell, ddpcrPlate, commonClassificationMethod, combinedCentres, clusterCentres, amplitudes, wellClassificationMethod<-, wellClassification<-, plateClassificationMethod<-, plateClassification<- ExportClasses: ddpcrWell, ddpcrPlate Package: tximeta Exports: addExons, addIds, getTximetaBFC, loadLinkedTxome, makeLinkedTxome, setTximetaBFC, tximeta ExportMethods: summarizeToGene Package: tximport Exports: makeCountsFromAbundance, summarizeToGene, tximport ExportMethods: summarizeToGene Package: TxRegInfra Exports: RaggedMongoExpt, URL_txregInAWS, URL_txregLocal, basicFormatter, dnmetaApp, getDocumentFields, getFieldNames, grConverter, importBedToMongo, listAllCollections, makeAggregator, makeColData, makeGRConverterList, sbov, sbov_to_graphNEL, txmodels, txregCollections, verifyHasMongoCmd, verifyRunningMongodb 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: Ularcirc Exports: Compatible_Annotation_DBs, Ularcirc, bsj_fastq_generate, bsj_to_circRNA_sequence Package: unifiedWMWqPCR Exports: as.matrix, coef, esttype, forestplot, getEstimate, getOrder, groupinfo, housekeeping, is.unsorted, logor, oddsRatio, orderedBy, plot, pval, ref, se, type, uWMW, unorder, vcov, volcanoplot, zval ExportMethods: vcov, unorder, sort, plot, order, names, esttype, coef, [ ExportClasses: uwmwRes, uwmwEstimate Package: UniProt.ws Exports: columns, availableUniprotSpecies, lookupUniprotSpeciesFromTaxId, UniProt.ws, taxname2domain, taxname2species, taxname2taxid, updatespecfile ExportMethods: keytypes, columns, keys, select, taxId, taxId<-, species Package: Uniquorn Exports: add_custom_vcf_to_database, identify_vcf_file, initiate_canonical_databases, read_library_names, remove_ccls_from_database, remove_library_from_database, show_contained_ccls, show_contained_variants_for_ccl, show_contained_variants_in_library, show_which_ccls_contain_variant Package: universalmotif Exports: add_gap, add_multifreq, as.data.frame, cbind, colMeans, colSums, colnames, compare_columns, compare_motifs, consensus_to_ppm, consensus_to_ppmAA, convert_motifs, convert_type, count_klets, create_motif, create_sequences, enrich_motifs, filter_motifs, get_bkg, get_consensus, get_consensusAA, get_klets, get_matches, get_scores, icm_to_ppm, log_string_pval, make_DBscores, merge_motifs, motif_peaks, motif_pvalue, motif_rc, motif_score, motif_tree, ncol, normalize, nrow, pcm_to_ppm, position_icscore, ppm_to_icm, ppm_to_pcm, ppm_to_pwm, pwm_to_ppm, read_cisbp, read_homer, read_jaspar, read_matrix, read_meme, read_motifs, read_transfac, read_uniprobe, rowMeans, rowSums, rownames, run_meme, sample_sites, scan_sequences, score_match, shuffle_motifs, shuffle_sequences, shuffle_string, subset, summarise_motifs, switch_alph, trim_motifs, ungap, view_motifs, write_homer, write_jaspar, write_matrix, write_meme, write_motifs, write_transfac ExportMethods: create_motif, convert_motifs ExportClasses: universalmotif Package: uSORT Exports: Rwanderlust, SPIN, STS_sortingcost, autoSPIN, driving_force_gene_selection, elbow_detection, monocle_wrapper, neighborhood_sortingcost, pca_gene_selection, sWanderlust, uSORT, uSORT_GUI, uSORT_preProcess, uSORT_sorting_wrapper, uSORT_write_results Package: variancePartition Exports: [.MArrayLM2, ESS, calcVarPart, canCorPairs, classifyTestsF, colinearityScore, dream, extractVarPart, fitExtractVarPartModel, fitVarPartModel, getContrast, getVarianceComponents, ggColorHue, plotCompareP, plotContrasts, plotCorrMatrix, plotCorrStructure, plotPercentBars, plotStratify, plotStratifyBy, plotVarPart, sortCols, varPartConfInf, voomWithDreamWeights ExportMethods: topTable, sortCols, residuals, plotVarPart, fitVarPartModel, fitExtractVarPartModel, eBayes, classifyTestsF, calcVarPart, as.matrix, as.data.frame, ESS ExportClasses: varPartResults, varParFrac, VarParFitList, VarParCIList, MArrayLM2 Package: VariantAnnotation Exports: VCF, VCFHeader, reference, header, header<-, meta, meta<-, vcfWhich, vcfWhich<-, vcfFixed, vcfFixed<-, vcfInfo, vcfInfo<-, vcfGeno, vcfGeno<-, vcfSamples, vcfSamples<-, vcfTrimEmpty, vcfTrimEmpty<-, duplicateRSID, CodingVariants, IntronVariants, FiveUTRVariants, ThreeUTRVariants, IntergenicVariants, SpliceSiteVariants, PromoterVariants, AllVariants, upstream, upstream<-, downstream, downstream<-, idType, idType<-, promoter, promoter<-, intergenic, intergenic<-, probabilityToSnpMatrix, GLtoGP, PLtoGP, VRanges, VRangesList, asVCF, softFilter, resetFilter, totalDepth, altDepth, refDepth, sampleNames, sampleNames<-, altFraction, softFilterMatrix, softFilterMatrix<-, hardFilters, hardFilters<-, called, stackSamples, altDepth<-, refDepth<-, totalDepth<-, probabilityToSnpMatrix, GLtoGP, readInfo, readGeno, readGT, genotypeCodesToNucleotides, tabulate, VRangesScanVcfParam, readVcfAsVRanges, isSNV, isInsertion, isDeletion, isIndel, isDelins, isTransition, isSubstitution, VcfFile, VcfFileList, makeVRangesFromGRanges ExportMethods: filterVcf, scanVcf, scanVcfHeader, ScanVcfParam, readVcf, writeVcf, expand, predictCoding, getTranscriptSeqs, getSeq, genotypeToSnpMatrix, snpSummary, locateVariants, summarizeVariants, isSNV, isInsertion, isDeletion, isIndel, isDelins, isTransition, isSubstitution, fixed, fixed<-, ref, ref<-, alt, alt<-, qual, qual<-, filt, filt<-, info, info<-, geno, geno<-, strand, strand<-, [, [<-, cbind, rbind, mcols<-, indexVcf, vcfFields, subset, genome, seqlevels, seqinfo, reference, samples, header, meta, keys, keytypes, columns, select, import Package: VariantExperiment Exports: VariantExperiment, gdsfile, loadVariantExperiment, makeVariantExperimentFromGDS, makeVariantExperimentFromVCF, saveVariantExperiment, showAvailable ExportMethods: titv, seqNumAllele, seqMissing, seqAlleleFreq, seqAlleleCount, refDosage, pca, meanBySample, isVariant, isSNV, inbreedCoeff, hwe, homozygosity, heterozygosity, countSingletons, altDosage ExportClasses: VariantExperiment Package: VariantFiltering Exports: VariantFilteringParam, spliceSiteMatricesHuman, reportVariants, variantLocations, readWm, readAAradicalChangeMatrix, FiveSpliceSiteVariants, ThreeSpliceSiteVariants, GenePhylostrataDb, browseVariants ExportMethods: summary, width, conservedPositions, wmName, wmScore, wmFilename, wmLocations, wmLocations<-, wmStrictLocations, wmStrictLocations<-, show, xLinked, autosomalRecessiveHomozygous, autosomalDominant, deNovo, autosomalRecessiveHeterozygous, unrelatedIndividuals, filters, filters<-, filtersMetadata, cutoffs, cutoffs<-, change<-, sortings, sortings<-, minIntronLength, minIntronLength<-, upstream, upstream<-, downstream, downstream<-, length, softFilterMatrix, softFilterMatrix<-, samples, samples<-, resetSamples, bamFiles, bamFiles<-, inheritanceModel, param, allVariants, filteredVariants, sog, annoGroups, dbSNPpresent, dbSNPpresent<-, OMIMpresent, OMIMpresent<-, variantType, variantType<-, variantLocation, variantLocation<-, variantConsequence, variantConsequence<-, aaChangeType, aaChangeType<-, MAFpop, MAFpop<-, naMAF, naMAF<-, maxMAF, maxMAF<-, minPhastCons, minPhastCons<-, minPhylostratum, minPhylostratum<-, minScore5ss, minScore5ss<-, minScore3ss, minScore3ss<-, minCUFC, minCUFC<-, genePhylostratum, genePhylostrata ExportClasses: FiveSpliceSiteVariants, ThreeSpliceSiteVariants, GenePhylostrataDb, VariantFilteringParam, VariantFilteringResults, WeightMatrix, CutoffsList Package: VariantTools Exports: callVariants, qaVariants, tallyVariants, postFilterVariants, MinTotalDepthFilter, calculateConcordanceMatrix, callVariantConcordance, calculateVariantConcordance, VariantQAFilters, VariantCallingFilters, VariantPostFilters, TallyVariantsParam, variantGR2Vcf, callSampleSpecificVariants, SampleSpecificVariantFilters, annotateWithControlDepth, SetdiffVariantsFilter, DepthFETFilter, MaxControlFreqFilter, callWildtype, minCallableCoverage, matchVariants, %variant_in%, extractCoverageForPositions, pileupVariants, CallGenotypesParam ExportMethods: callGenotypes Package: vbmp Exports: vbmp, predictCPP, predError, predLik, predClass, covParams, plotDiagnostics Package: VCFArray Exports: VCFArray, coerce, vcffile ExportMethods: vcffile, show, rowRanges, extract_array, dimnames, dim ExportClasses: VCFMatrix, VCFArray Package: Vega Exports: vega, plotSegmentation Package: VegaMC Exports: vegaMC, sortData Package: VennDetail Exports: detail, dplot, getFeature, getSet, make.subset, result, rowjoin, setcolor, venndetail, vennpie ExportMethods: vennpie, rowjoin, result, getSet, getFeature, dplot, detail ExportClasses: Venn Package: vidger Exports: vsBoxPlot, vsDEGMatrix, vsFourWay, vsMAMatrix, vsMAPlot, vsScatterMatrix, vsScatterPlot, vsVolcano, vsVolcanoMatrix Package: viper Exports: aREA, approxk2d, aracne2regulon, aracne2regulon4cnv, bootstrapTtest, bootstrapmsviper, distMode, fcvarna, filterCV, filterColMatrix, filterRowMatrix, frcv, frvarna, integrateSignatures, ledge, msviper, msviperAnnot, msviperClass, msviperCombinatorial, msviperSynergy, pruneRegulon, rowTtest, scaleGroups, shadow, signatureDistance, ttestNull, viper, viperRPT, viperSignature, viperSimilarity Package: ViSEAGO Exports: Bioconductor2GO, Custom2GO, Ensembl2GO, EntrezGene2GO, EntrezGene_orthologs, Uniprot2GO, overLapper, pkgdiagram, taxonomy ExportMethods: show_table, show_heatmap, merge_enrich_terms, create_topGOdata, compute_SS_distances, compare_clusters, clusters_cor, build_GO_SS, available_organisms, annotate, Upset, MDSplot, GOterms_heatmap, GOcount, GOclusters_heatmap Package: vsn Exports: vsnMatrix, justvsn, vsnrma, sagmbAssess, sagmbSimulateData, plotVsnLogLik, scalingFactorTransformation ExportMethods: vsn2, meanSdPlot, predict, logLik, coef, coefficients, show, exprs, nrow, ncol, dim, coerce ExportClasses: vsn, vsnInput Package: vulcan Exports: average_fragment_length, corr2p, densityauc, dpareto, fisherp, gsea, kmgformat, null_gsea, p2corr, p2z, pareto.fit, plot_gsea, ppareto, rea, slice, stouffer, textplot2, val2col, vulcan, vulcan.annotate, vulcan.import, vulcan.normalize, vulcan.pathways, wstouffer, z2p Package: waddR Exports: permutations, squared_wass_approx, squared_wass_decomp, testZeroes, wasserstein.sc, wasserstein.test, wasserstein_metric Package: wateRmelon ExportMethods: naten, betaqn, nanet, nanes, danes, danet, daten1, daten2, nasen, dasen, danen, tost, fuks, swan, colnames, seabi, dmrse, dmrse_row, dmrse_col, genki, pfilter, bscon Package: wavClusteR Exports: readSortedBam, getAllSub, fitMixtureModel, getExpInterval, getHighConfSub, getClusters, filterClusters, annotateClusters, plotSizeDistribution, plotStatistics, getMetaGene, getMetaTSS, plotSubstitutions, estimateFDR, exportClusters, exportHighConfSub, exportCoverage, exportSequences 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: Wrench Exports: wrench Package: XBSeq Exports: XBSeqDataSet, XBSeqTest, XBSeq, getSignalVars, MAplot, plotSCVEsts, XBplot ExportMethods: conditions, conditions<-, dispEst, dispEst<-, dispTable, estimateSCV, fitInfo, counts, estimateRealCount ExportClasses: XBSeqDataSet Package: XCIR Exports: addAnno, annotateX, betaBinomXI, betaParam, consensusXCI, getGenicDP, getXCIstate, mart_genes, plotQC, readRNASNPs, readVCF4, readXCI, sample_clean Package: xcms Exports: etg, medianFilter, plotQC, retexp, specNoise, specPeaks, SSgauss, msn2xcmsRaw, verify.mzQuantML, xcmsRaw, xcmsSet, xcmsFragments, xcmsPapply, phenoDataFromPaths, binYonX, breaks_on_binSize, breaks_on_nBins, do_findChromPeaks_centWave, do_findChromPeaks_massifquant, do_findChromPeaks_matchedFilter, do_findPeaks_MSW, do_findChromPeaks_centWaveWithPredIsoROIs, do_findChromPeaks_addPredIsoROIs, imputeLinInterpol, useOriginalCode, setAs, do_groupChromPeaks_density, do_groupPeaks_mzClust, do_groupChromPeaks_nearest, do_adjustRtime_peakGroups, processHistoryTypes, adjustRtimePeakGroups, plotAdjustedRtime, plotChromatogram, highlightChromPeaks, plotChromPeaks, plotChromPeakImage, isCalibrated, plotMsData, applyAdjustedRtime, filterFeatureDefinitions, peaksWithMatchedFilter, peaksWithCentWave, rla, rowRla, featureSummary, overlappingFeatures, fixedMz, fixedRt, exportMetaboAnalyst, imputeRowMin, imputeRowMinRand, chromPeakSpectra, featureSpectra, featureChromatograms, hasFilledChromPeaks, findChromPeaksIsolationWindow, reconstructChromPeakSpectra, CentWaveParam, MatchedFilterParam, MassifquantParam, MSWParam, CentWavePredIsoParam, PeakDensityParam, MzClustParam, NearestPeaksParam, PeakGroupsParam, ObiwarpParam, GenericParam, FillChromPeaksParam, CalibrantMassParam, XChromatogram, XChromatograms ExportMethods: hasChromPeaks, hasFilledChromPeaks, hasFeatures, hasAdjustedRtime, adjustedRtime, adjustedRtime<-, featureDefinitions, featureDefinitions<-, featureValues, chromPeaks, chromPeaks<-, chromPeakData, chromPeakData<-, processHistory, fileIndex, processDate, processInfo, processParam, processType, bin, clean, filterAcquisitionNum, filterFile, filterMsLevel, filterMz, filterRt, normalize, pickPeaks, removePeaks, smooth, dropAdjustedRtime, dropFeatureDefinitions, dropChromPeaks, spectra, rtime, mz, intensity, extractChromatograms, fillChromPeaks, dropFilledChromPeaks, extractMsData, chromatogram, spectrapply, writeMSData, plotChromPeakDensity, align, correlate, plot, ppm, ppm<-, peakwidth, peakwidth<-, snthresh, snthresh<-, prefilter, prefilter<-, mzCenterFun, mzCenterFun<-, integrate, integrate<-, mzdiff, mzdiff<-, fitgauss, fitgauss<-, noise, noise<-, verboseColumns, verboseColumns<-, roiList, roiList<-, firstBaselineCheck, firstBaselineCheck<-, roiScales, binSize, binSize<-, impute, impute<-, baseValue, baseValue<-, distance, distance<-, fwhm, fwhm<-, sigma, sigma<-, max, max<-, steps, steps<-, index, index<-, criticalValue, criticalValue<-, consecMissedLimit, consecMissedLimit<-, unions, unions<-, checkBack, checkBack<-, withWave, withWave<-, scales, scales<-, nearbyPeak, nearbyPeak<-, peakScaleRange, peakScaleRange<-, ampTh, ampTh<-, minNoiseLevel, minNoiseLevel<-, ridgeLength, ridgeLength<-, peakThr, peakThr<-, tuneIn, tuneIn<-, addParams, addParams<-, snthreshIsoROIs, snthreshIsoROIs<-, maxCharge, maxCharge<-, maxIso, maxIso<-, mzIntervalExtension, mzIntervalExtension<-, polarity, polarity<-, sampleGroups, sampleGroups<-, bw, bw<-, minFraction, minFraction<-, minSamples, minSamples<-, maxFeatures, maxFeatures<-, absMz, absMz<-, absRt, absRt<-, mzVsRtBalance, mzVsRtBalance<-, kNN, kNN<-, extraPeaks, extraPeaks<-, smooth<-, span, span<-, family, family<-, peakGroupsMatrix, peakGroupsMatrix<-, centerSample, centerSample<-, response, response<-, distFun, distFun<-, gapInit, gapInit<-, gapExtend, gapExtend<-, factorDiag, factorDiag<-, factorGap, factorGap<-, localAlignment, localAlignment<-, initPenalty, initPenalty<-, expandMz, expandMz<-, expandRt, expandRt<-, subset, subset<-, subsetAdjust, subsetAdjust<-, dirname, dirname<-, showError, findChromPeaks, groupChromPeaks, adjustRtime, [, $, [[, split, absent, AutoLockMass, calibrate, collect, deepCopy, filepaths, filepaths<-, diffreport, findMZ, findneutral, fillPeaks, fillPeaks.MSW, fillPeaks.chrom, findPeaks.centWave, findPeaks.addPredictedIsotopeFeatures, findPeaks.centWaveWithPredictedIsotopeROIs, findPeaks.massifquant, findPeaks.matchedFilter, findPeaks.MSW, findPeaks, getEIC, getPeaks, getScan, getMsnScan, getSpec, getXcmsRaw, group, group.density, group.mzClust, group.nearest, groupidx, groupidx<-, groupnames, groups, groups<-, groupval, image, levelplot, mslevel, mzrange, peaks, peaks<-, peakTable, phenoData, phenoData<-, plotChrom, plotEIC, plotPeaks, plotRaw, plotrt, plotScan, plotSpec, plotSurf, plotTIC, plotTree, present, profinfo, profinfo<-, profMat, profMedFilt, profMethod, profMethod<-, profMz, profRange, profStep, profStep<-, progressCallback, progressCallback<-, rawEIC, rawMat, retcor, retcor.peakgroups, retcor.obiwarp, revMz, rtrange, sampclass, sampclass<-, sampnames, sampnames<-, scanrange, specDist, specDist.cosine, specDist.meanMZmatch, specDist.peakCount, show, sortMz, stitch, updateObject, write.cdf, write.mzdata, write.mzQuantML, xcmsSource, loadRaw, isolationWindowTargetMz ExportClasses: XCMSnExp, ProcessHistory, XProcessHistory, XChromatogram, XChromatograms, CentWaveParam, MatchedFilterParam, MassifquantParam, MSWParam, CentWavePredIsoParam, PeakDensityParam, MzClustParam, NearestPeaksParam, PeakGroupsParam, ObiwarpParam, GenericParam, FillChromPeaksParam, CalibrantMassParam, xcmsEIC, xcmsPeaks, xcmsRaw, xcmsSet, xcmsFragments, xcmsSource, xcmsFileSource Package: XDE Exports: calculatePosteriorAvg, empiricalStart, ssStatistic, symbolsInteresting, xde, xsScores ExportMethods: [, [[, $, bayesianEffectSize, bayesianEffectSize<-, burnin, burnin<-, calculateBayesianEffectSize, firstMcmc, firstMcmc<-, coerce, dim, directory, directory<-, featureData, featureNames, geneCenter, hyperparameters, hyperparameters<-, initialize, iterations, iterations<-, lapply, lastMcmc, lastMcmc<-, notes, nrow, nSamples, output, output<-, pData, phenotypeLabel, phenotypeLabel<-, plot, posteriorAvg, posteriorAvg<-, savedIterations, seed, seed<-, show, showIterations, showIterations<-, .standardizedDelta, standardizeSamples, studyCenter, studyNames, studyNames<-, thin, thin<-, tuning, tuning<-, updates, updates<-, zeroNu ExportClasses: ExpressionSetList, XdeParameter, XdeMcmc Package: Xeva Exports: ABC, AUC, TGI, angle, createXevaSet, dosePlot, downloadXevaSet, drugSensitivitySig, getMolecularProfiles, lmm, mRECIST, plotBatch, plotPDX, plotmRECIST, response, sensitivity, setResponse, slope, subsetXeva, summarizeMolecularProfiles, summarizeResponse, waterfall ExportMethods: selectModelIds, modelInfo, getExperiment, drugInform, batchInfo, addExperimentalDesign Package: XINA Exports: alluvial_enriched, draw_alluvial_plot, get_comigrations_by_name, get_condition_biased_comigrations, get_unknown_ppi_nodes, load_previous_results, make_random_xina_data, mutate_colors, plot_clusters, plot_clusters_all, plot_condition_compositions, plot_enrichment_results, xina_analysis, xina_clustering, xina_enrichment, xina_plot_all, xina_plot_bycluster, xina_plot_single Package: xmapbridge Exports: xmap.debug, xmap.plot, xmap.points, xmap.col, xmap.project.new, xmap.project.load, xmap.project.list, xmap.project.save, xmap.project.delete, xmap.graph.new, xmap.graph.load, xmap.graph.list, xmap.graph.save, xmap.graph.delete, xmap.plot.new, xmap.plot.load, xmap.plot.list, xmap.plot.save, xmap.plot.delete Package: xps Exports: import.expr.scheme, import.exon.scheme, import.genome.scheme, import.data, export.scheme, export.data, export.expr, export.call, export.filter, export.root, rma, mas4, mas5, mas5.call, dabg.call, dfw, farms, ini.call, firma, firma.expr, firma.score, trma, bgcorrect, normalize, summarize, express, qualify, bgcorrect.mas4, bgcorrect.mas5, bgcorrect.rma, bgcorrect.gc, normalize.constant, normalize.quantiles, normalize.lowess, normalize.supsmu, summarize.mas4, summarize.mas5, summarize.rma, qualify.rlm, fitQC, fitRLM, rmaPLM, AffyRNAdeg, summaryAffyRNAdeg, plotAffyRNAdeg, prefilter, unifilter, plotBoxplot, plotDensity, plotImage, plotPM, plotProbeset, plotIntensity2GC, plotCorr, plotMAD, plotMA, plotNUSE, plotPCA, plotRLE, plotCall, plotBorder, plotCOI, plotVolcano, ProjectInfo, PreFilter, UniFilter, xpsQAReport, root.scheme, root.data, root.merge.data, root.expr, root.call, root.density, root.image, root.profile, root.graph1D, root.graph2D, root.mvaplot, root.hist1D, root.hist2D, root.hist3D, xpsOptions, debug.xps, getDatatype, validTreetype, getChipName, getChipType, getNameType, getProbeInfo, getNumberTrees, getTreeNames, isROOTFile, existsROOTFile, type2Exten, exonLevel, extenPart, namePart, metaProbesets ExportMethods: filterTreeset, validFilter, volcanoplot, callTreeset, exprTreeset, fcFilter, fcFilter<-, unitestFilter, unitestFilter<-, uniTest, uniTest<-, callFilter, callFilter<-, cvFilter, cvFilter<-, diffFilter, diffFilter<-, gapFilter, gapFilter<-, highFilter, highFilter<-, lowFilter, lowFilter<-, madFilter, madFilter<-, quantileFilter, quantileFilter<-, ratioFilter, ratioFilter<-, varFilter, varFilter<-, numberFilters, borderplot, borders, coiplot, NUSE, qualOption, qualOption<-, qualType, qualType<-, residuals, RLE, weights, xpsRNAdeg, attachCall, attachPVal, pvalData, pvalData<-, presCall, presCall<-, removeCall, removePVal, validCall, validPVal, callplot, attachExpr, corplot, exprs, exprs<-, exprType, exprType<-, madplot, mvaplot, normType, normType<-, nuseplot, pcaplot, rleplot, removeExpr, se.exprs, validExpr, validSE, xpsPreFilter, xpsUniFilter, addData, attachBgrd, attachDataXY, attachInten, background, background<-, bgtreeNames, indexUnits, intensity, intensity<-, intensity2GCplot, mm, mmindex, pm, pmindex, pmplot, probesetplot, rawCELName, removeBgrd, removeDataXY, removeInten, validBgrd, xpsBgCorrect, xpsDABGCall, xpsFIRMA, xpsINICall, xpsMAS4, xpsMAS5, xpsMAS5Call, xpsNormalize, xpsPreprocess, xpsQualify, xpsQualityControl, xpsSummarize, xpsRMA, attachData, boxplot, getTreeData, hist, image, mboxplot, removeData, schemeFile, schemeFile<-, schemeSet, schemeSet<-, treeData, validData, attachMask, attachProbe, attachProbeContentGC, attachProbeSequence, attachUnitNames, chipMask, chipMask<-, chipName, chipProbe, chipProbe<-, chipType, chipType<-, ncols, nrows, probeContentGC, probeInfo, probeSequence, probesetID2unitID, removeMask, removeProbe, removeProbeContentGC, removeProbeSequence, removeUnitNames, transcriptID2unitID, symbol2unitID, unitID2probesetID, unitID2symbol, unitID2transcriptID, unitNames, unitNames<-, export, fileDir, fileDir<-, initialize, root.browser, rootFile, rootFile<-, setName, setName<-, setType, setType<-, treeInfo, treeNames, arrayInfo, arrayInfo<-, authorInfo, authorInfo<-, biopsyInfo, biopsyInfo<-, cellineInfo, cellineInfo<-, datasetInfo, datasetInfo<-, hybridizInfo, hybridizInfo<-, primcellInfo, primcellInfo<-, projectInfo, projectInfo<-, sampleInfo, sampleInfo<-, show, sourceInfo, sourceInfo<-, tissueInfo, tissueInfo<-, treatmentInfo, treatmentInfo<- ExportClasses: ProjectInfo, TreeSet, Filter, PreFilter, UniFilter, SchemeTreeSet, ProcesSet, DataTreeSet, ExprTreeSet, CallTreeSet, FilterTreeSet, AnalysisTreeSet Package: XVector Exports: duplicated.XRawList, open_input_files, SharedVector.compare, SharedVector.copy, SharedRaw, SharedRaw.readInts, SharedRaw.writeInts, SharedRaw.read, SharedRaw.write, SharedRaw.readComplexes, XRaw, XInteger, XDouble, XNumeric, XVectorList, unsplit_list_of_XVectorList, RdaCollection, subseq, subseq<-, rdaPath, xvcopy, compact, reverse ExportMethods: subseq, subseq<-, rdaPath, xvcopy, compact, reverse, length, names, names<-, [, [<-, [[, [[<-, rev, as.vector, as.integer, as.numeric, as.raw, as.data.frame, toString, coerce, c, show, ==, !=, <=, duplicated, match, order, rank, is.unsorted, relist, width, updateObject, showAsCell, bindROWS, parallelSlotNames, pcompare, elementNROWS, relistToClass, Views, viewMins, viewMaxs, viewSums, viewMeans, viewWhichMins, viewWhichMaxs, extractList, windows, slice ExportClasses: SharedVector, SharedVector_Pool, SharedRaw, SharedRaw_Pool, SharedInteger, SharedDouble, XVector, XRaw, XInteger, XDouble, GroupedIRanges, XVectorList, XRawList, XIntegerViews, RdaCollection Package: yamss Exports: readMSdata, bakedpi, slicepi, CMSslice, getTIC, getEICS, diffrep, plotDensityRegion, densityEstimate, densityCutoff, densityQuantiles, peakBounds, peakQuants ExportMethods: show, colData ExportClasses: CMSraw, CMSproc, CMSslice Package: YAPSA Exports: LCD, LCD_complex_cutoff, LCD_complex_cutoff_perPID, add_annotation, add_as_fist_to_list, aggregate_exposures_by_category, annotate_intermut_dist_PID, annotate_intermut_dist_cohort, annotation_exposures_barplot, annotation_heatmap_exposures, attribute_nucleotide_exchanges, average_over_present, build_gene_list_for_pathway, compare_SMCs, compare_exposures, compare_sets, compare_to_catalogues, complex_heatmap_exposures, compute_comparison_stat_df, cosineDist, create_mutation_catalogue_from_VR, create_mutation_catalogue_from_df, cut_breaks_as_intervals, exposures_barplot, extract_names_from_gene_list, find_affected_PIDs, get_extreme_PIDs, hclust_exposures, makeVRangesFromDataFrame, make_catalogue_strata_df, make_comparison_matrix, make_strata_df, make_subgroups_df, melt_exposures, merge_exposures, normalizeMotifs_otherRownames, normalize_df_per_dim, plotExchangeSpectra, plot_SMC, plot_exposures, plot_relative_exposures, plot_strata, repeat_df, run_SMC, run_annotate_vcf_pl, run_comparison_catalogues, run_comparison_general, run_kmer_frequency_correction, run_kmer_frequency_normalization, run_plot_strata_general, sd_over_present, shapiro_if_possible, split_exposures_by_subgroups, stat_plot_subgroups, stat_test_SMC, stat_test_subgroups, stderrmean, stderrmean_over_present, sum_over_list_of_df, test_exposureAffected, test_gene_list_in_exposures, transform_rownames_MATLAB_to_R, transform_rownames_R_to_MATLAB, transform_rownames_YAPSA_to_deconstructSigs, transform_rownames_deconstructSigs_to_YAPSA, transform_rownames_nature_to_R, translate_to_1kG, translate_to_hg19, trellis_rainfall_plot 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 Package: yarn Exports: annotateFromBiomart, checkMisAnnotation, checkTissuesToMerge, downloadGTEx, filterGenes, filterLowGenes, filterMissingGenes, filterSamples, normalizeTissueAware, plotCMDS, plotDensity, plotHeatmap Package: zFPKM Exports: zFPKM, zFPKMPlot Package: zinbwave Exports: computeDevianceResiduals, computeObservationalWeights, getAlpha_mu, getAlpha_pi, getBeta_mu, getBeta_pi, getEpsilon_W, getEpsilon_alpha, getEpsilon_beta_mu, getEpsilon_beta_pi, getEpsilon_gamma_mu, getEpsilon_gamma_pi, getEpsilon_zeta, getGamma_mu, getGamma_pi, getLogMu, getLogitPi, getMu, getPhi, getPi, getTheta, getV_mu, getV_pi, getW, getX_mu, getX_pi, getZeta, glmWeightedF, imputeZeros, loglik, nFactors, nFeatures, nParams, nSamples, orthogonalizeTraceNorm, penalty, solveRidgeRegression, zinb.loglik, zinb.loglik.dispersion, zinb.loglik.dispersion.gradient, zinb.loglik.regression, zinb.loglik.regression.gradient, zinbAIC, zinbBIC, zinbFit, zinbInitialize, zinbModel, zinbOptimize, zinbOptimizeDispersion, zinbSim, zinbsurf, zinbwave ExportMethods: zinbwave, zinbsurf, zinbSim, zinbFit, zinbBIC, zinbAIC, show, penalty, nSamples, nParams, nFeatures, nFactors, loglik, getZeta, getX_pi, getX_mu, getW, getV_pi, getV_mu, getTheta, getPi, getPhi, getMu, getLogitPi, getLogMu, getGamma_pi, getGamma_mu, getEpsilon_zeta, getEpsilon_gamma_pi, getEpsilon_gamma_mu, getEpsilon_beta_pi, getEpsilon_beta_mu, getEpsilon_alpha, getEpsilon_W, getBeta_pi, getBeta_mu, getAlpha_pi, getAlpha_mu ExportClasses: ZinbModel