Package: allenpvc Exports: allenpvc Package: aracne.networks Exports: write.regulon Package: AssessORFData Exports: GetDataMapObj, GetGeneSources, GetResultsObj, GetStrainIDs, SaveGenomeToPath Package: biscuiteerData Exports: biscuiteerDataCacheAll, biscuiteerDataGet, biscuiteerDataList, biscuiteerDataListDates Package: BloodCancerMultiOmics2017 Exports: meltWholeDF, whichInGrob, safeMatch, stripConc, deckel, pheatmapwh, giveDrugLabel, toCaps, scientific_10, percentAxisScale, col2hex, defineResponseGroups, log10div, exp10div, smunlist, moround, nrisk, addNrisk, survplot Package: cgdv17 Exports: getRVS, getrd, countVariants, variantNames, padToReference ExportMethods: show, sampleNames, variantGRanges ExportClasses: raggedVariantSet Package: chipseqDBData Exports: CBPData, H3K27me3Data, H3K4me3Data, H3K9acData, NFYAData Package: CopyNeutralIMA Exports: getCopyNeutralRGSet Package: curatedBreastData Exports: processExpressionSetList, processExpressionSet, filterAndImputeSamples, collapseDupProbes, removeDuplicatedPatients, filterGenesByVariance Package: curatedMetagenomicData Exports: ExpressionSet2MRexperiment, ExpressionSet2phyloseq, cmdValidVersions, curatedMetagenomicData, getMetaphlanTree, mergeData Package: curatedTCGAData Exports: curatedTCGAData Package: DAPARdata Exports: DAPARdata Package: davidTiling Exports: getAttributeField, getAllGO, showDens, GOHyperG, scatterWithHist Package: depmap Exports: depmap_release, depmap_rnai Package: DeSousa2013 Exports: buildClassifier, compGapStats, conClust, filterDiffGenes, filterSamples, findDiffGenes, geneExpPre, pamClassify, pbs2unigenes, progAMC, selTopVarGenes, CRCPipeLine, figGAP, figSilh, figPAMCV, figClassify, figKM Package: DmelSGI Exports: getBaseDir, applyDimensionReduction, callInteractions, estimatePairwiseInteractions, orderSpiderAxis, grid.spider, grid.spider.legend, toRaster, toMatrix, orderDim, trsf, myHeatmap, hrNames, learnCoComplexFct, convertCorrelations, mymedpolish, plotPIdata, plot2Phenotypes, plotHairballLabels, selectByStability, subSampleForStabilitySelectionFct Package: dsQTL Exports: getSNPlocs, SE2ES Package: DuoClustering2018 Exports: plot_entropy, plot_k_diff, plot_performance, plot_stability, plot_timing Package: EGSEAdata Exports: egsea.data Package: fabiaData Exports: fabiaDataVersion, fabiaData Package: Fletcher2013a Exports: Fletcher2013pipeline.limma, Fletcher2013pipeline.deg, Fletcher2013pipeline.pca, Fletcher2013pipeline.supp Package: Fletcher2013b Exports: Fletcher2013pipeline.mra1st, Fletcher2013pipeline.mra2nd, Fletcher2013pipeline.mraNormals, Fletcher2013pipeline.mraTALL, Fletcher2013pipeline.synergyShadow, Fletcher2013pipeline.consensusnet, Fletcher2013pipeline.enrichmap, Fletcher2013gsea.regulons Package: flowPloidyData Exports: flowPloidyFiles, fpVac, fpBad Package: FlowSorted.Blood.EPIC Exports: estimateCellCounts2 Package: furrowSeg Exports: area2px, constructBox, identifyFurrowPosition, identifyTimeMinArea, isOdd, isolateBoxCells, makeOdd, microns2px, plotFeatureEvolution, px2area, px2microns, segmentFurrowAllStacks Package: geuvStore2 Exports: makeGeuvStore2, g17transRegistry, g18transRegistry Package: harbChIP Exports: chkAllUS, chkMotif4TF, getUpstream, allhex, buildUpstreamSeqs2 ExportMethods: show, keys, seqs, organism, Nmers ExportClasses: upstreamSeqs Package: HCAData Exports: HCAData Package: HD2013SGI Exports: HD2013SGImaineffects, HD2013SGIselectByStability, HD2013SGIorderDim, HD2013SGIHeatmapHuman Package: Hiiragi2013 Exports: pamCluster, plotProjection, myHeatmap, myHeatmap2, MDSplot, getDifferentialExpressedGenes Package: HMP16SData Exports: %>%, as_phyloseq, attach_dbGaP, kable_one, table_one Package: HMP2Data Exports: IBD16S, T2D16S, momspi16S, momspiCytokines, momspiMultiAssay, patient_table, table_two, visit_table Package: IHWpaper Exports: analyze_dataset, bh, bonf, clfdr, continuous_wrap, ddhf, du_ttest_sim, du_ttest_sim_fun, gbh, ihw_5fold, ihw_5fold_reg, ihw_bonf_5fold_reg, ihw_ecdf_5fold, ihw_naive, ihw_storey_5fold, lsl_gbh, lsl_pi0_est, null_sim, null_sim_fun, pretty_legend, run_evals, storey_qvalue, stratified_bh, tst_gbh, tst_pi0_est, wasserman_normal_prds_sim, wasserman_normal_prds_sim_fun, wasserman_normal_sim, wasserman_normal_sim_fun Package: JASPAR2014 ExportClasses: JASPAR2014 Package: JASPAR2016 ExportClasses: JASPAR2016 Package: leeBamViews ExportMethods: tabulateReads, totalReadCounts Package: LungCancerLines Exports: LungCancerFastqFiles, LungCancerBamFiles Package: MetaGxBreast Exports: loadBreastDatasets, loadBreastEsets Package: MetaGxOvarian Exports: loadOvarianDatasets, loadOvarianEsets Package: MetaGxPancreas Exports: loadPancreasDatasets, loadPancreasEsets Package: mitoODEdata Exports: readspot, plotspot, getanno, getspot, getsirna Package: MMAPPR2data Exports: exampleMutBam, exampleWTbam, goldenFasta, goldenGFF Package: MMDiffBamSubset Exports: Cfp1.Exp, WT.AB2, Null.AB2, Resc.AB2, Input, WT.AB2.Peaks, Null.AB2.Peaks, Resc.AB2.Peaks Package: MouseGastrulationData Exports: AtlasSampleMetadata, EmbryoAtlasData, EmbryoCelltypeColours, Tal1ChimeraData, WTChimeraData Package: msdata Exports: proteomics, ident, quant Package: msqc1 ExportClasses: msqc1 Package: MTseekerData Exports: .onAttach Package: Mulder2012 Exports: Mulder2012.pipeline, Mulder2012.fig, Mulder2012.PPIPre, Mulder2012.RNAiPre, Mulder2012.BMfitting, Mulder2012.BMfitting.extended, Mulder2012.InferPAN, Mulder2012.ModuleSearchByPvclust, Mulder2012.PPIenrich, Mulder2012.module.visualize, GSEARandomWalkFig, Arora2010.pipeline, Arora2010.fig, Arora2010.BMfitting, Arora2010.InferPAN, Arora2010.ModuleSearchByPvclust, Arora2010.hypergeo, Arora2010.module.visualize, dist.pvclust4PAN, parPvclust4PAN Package: NestLink Exports: .ssrc.mascot, NB.unambiguous, NB.unique, compose_GPGx8cTerm, compose_GPx10R, compose_GSx7cTerm, getExperimentHubFilename, getFC, getNB, nanobodyFlycodeLinking.as.fasta, nanobodyFlycodeLinking.summary, plot_in_silico_LCMS_map, runNGSAnalysis, twoPatternReadFilter Package: pasillaBamSubset Exports: untreated1_chr4, untreated3_chr4, dm3_chr4 Package: pd.atdschip.tiling Exports: pd.atdschip.tiling Package: pRolocdata Exports: pRolocdata, pRolocmetadata, print.pRolocmetadata Package: RegParallel Exports: RegParallel, glmParallel, lmParallel, coxphParallel, clogitParallel, glm.nbParallel, bayesglmParallel Package: restfulSEData Exports: dataResource Package: RforProteomics Exports: RProtVis, RProtViz, RforProteomics, analyse, analyze, detect, downloadData, massSpectrometryDataPackages, massSpectrometryPackages, new_ions, proteomicsPackages, spectrum Package: RNAinteractMAPK Exports: MAPK.predict.classification, MAPK.cv.classifier, MAPK.plot.classification, MAPK.smooth.scatter, MAPK.screen.as.array, MAPK.cv.TPS, MAPK.estimate.TPS, MAPK.plot.TPS.single, MAPK.plot.TPS.all, MAPK.plot.heatmap.raster, MAPK.report.gene.lists.paper Package: RNAseqData.HNRNPC.bam.chr14 Exports: RNAseqData.HNRNPC.bam.chr14_RUNNAMES, RNAseqData.HNRNPC.bam.chr14_BAMFILES Package: scRNAseq Exports: AztekinTailData, BachMammaryData, BaronPancreasData, BuettnerESCData, CampbellBrainData, ChenBrainData, GrunHSCData, GrunPancreasData, KolodziejczykESCData, LaMannoBrainData, LawlorPancreasData, LengESCData, LunSpikeInData, MacoskoRetinaData, MarquesBrainData, MessmerESCData, MuraroPancreasData, NestorowaHSCData, ReprocessedAllenData, ReprocessedFluidigmData, ReprocessedTh2Data, RichardTCellData, RomanovBrainData, SegerstolpePancreasData, ShekharRetinaData, TasicBrainData, UsoskinBrainData, XinPancreasData, ZeiselBrainData Package: sesameData Exports: sesameDataCacheAll, sesameDataGet, sesameDataList, sesameDataListDates Package: signatureSearchData Exports: combineNormRes, combineResults, getCmapCEL, inst_filter, meanExpr, meanExpr2h5, normalizeCel, probe2gene, runLimma, sampleList, sig_filter Package: SNAGEEdata Exports: getCC Package: synapterdata Exports: getHDMSeFinalPeptide, getMSeFinalPeptide, getMSePep3D, loadMaster, getMaster, getFasta, synobj2RData Package: systemPipeRdata Exports: pathList, genWorkenvir Package: tartare Exports: getFilename Package: TBX20BamSubset Exports: getBamFileList Package: TENxBrainData Exports: TENxBrainData, TENxBrainData20k Package: TENxBUSData Exports: TENxBUSData Package: TENxPBMCData Exports: TENxPBMCData Package: TimerQuant Exports: signal, fitCV, genRatioHeatmap, genTimeSteadyStateHeatmap, getBreaks10, getSpacedSeq, plotPrimordiumProfile, ratioSteadyState, ratioTimeDependent, simulatedSignal, simulatedSignalN, simulatedRatio, tss, x0ss, x1, x1ss, x1fretFP1, x1fretFP1ss, runChooseFP2App, runTimerModellingApp Package: topdownrdata Exports: topDownDataPath Package: VariantToolsData Exports: sumDepths, TP53Region Package: vulcandata Exports: vulcanexample, vulcansheet