Package: cgdv17 Exports: getRVS, getrd, countVariants, variantNames, padToReference ExportMethods: show, sampleNames, variantGRanges ExportClasses: raggedVariantSet Package: chipenrich.data ExportClasses: GeneSet, LocusDefinition Package: davidTiling Exports: getAttributeField, getAllGO, showDens, GOHyperG, scatterWithHist Package: DeSousa2013 Exports: buildClassifier, compGapStats, conClust, filterDiffGenes, filterSamples, findDiffGenes, geneExpPre, pamClassify, pbs2unigenes, progAMC, selTopVarGenes, CRCPipeLine, figGAP, figSilh, figPAMCV, figClassify, figKM Package: dsQTL Exports: getSNPlocs, SE2ES Package: encoDnaseI Exports: juxtaPlot ExportMethods: initialize, dataVals, getTrkXY, rangeLocs, chromStarts, clipTrk, [, chrnum ExportClasses: hg18track, chrnum 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.masters, Fletcher2013pipeline.siRNA, Fletcher2013pipeline.synergyShadow, Fletcher2013pipeline.consensusnet, Fletcher2013pipeline.enrichmap, Fletcher2013pipeline.motifs, Fletcher2013pipeline.chipseq, Fletcher2013mra.agreement.cohort1, Fletcher2013mra.agreement.exp1, Fletcher2013mra.agreement.exp2, Fletcher2013mra.agreement.exp3, Fletcher2013mra.heatmap1, Fletcher2013mra.heatmap2, Fletcher2013mra.consensus, Fletcher2013gsea.regulons Package: ggtut Exports: observed17ceu, onePerm17ceu, tr17_1_9, tr17_1_9_perm, hg18tx, getFixedBFL Package: harbChIP Exports: chkAllUS, chkMotif4TF, getUpstream, allhex, buildUpstreamSeqs2 ExportMethods: show, keys, seqs, organism, Nmers ExportClasses: upstreamSeqs Package: HD2013SGI Exports: HD2013SGImaineffects, HD2013SGIselectByStability, HD2013SGIorderDim, HD2013SGIHeatmapHuman Package: Hiiragi2013 Exports: pamCluster, plotProjection, myHeatmap, myHeatmap2, MDSplot, getDifferentialExpressedGenes Package: JASPAR2014 ExportClasses: JASPAR2014 Package: leeBamViews ExportMethods: tabulateReads, totalReadCounts Package: LungCancerLines Exports: LungCancerFastqFiles, LungCancerBamFiles Package: MafDb.ALL.wgs.phase1.release.v3.20101123 Exports: makeMafDbPackageKG, MafDbKGdefaultURL, MafDbKGdefaultPkgName Package: MafDb.ESP6500SI.V2.SSA137.dbSNP138 Exports: makeMafDbPackageESP, MafDbESPdefaultURL, MafDbESPdefaultPkgName Package: mitoODEdata Exports: readspot, plotspot, getanno, getspot, getsirna Package: MMDiffBamSubset Exports: Cfp1.Exp, WT.AB2, Null.AB2, Resc.AB2, Input, WT.AB2.Peaks, Null.AB2.Peaks, Resc.AB2.Peaks 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: pasillaBamSubset Exports: untreated1_chr4, untreated3_chr4, dm3_chr4 Package: pd.atdschip.tiling Exports: pd.atdschip.tiling Package: pRolocdata Exports: pRolocdata Package: RforProteomics Exports: getPXD000001mzXML, getPXD000001mzTab, getPXD000001mzData, getThermoHelaPRTC, downloadData, RforProteomics, proteomicsPackages, massSpectrometryPackages, massSpectrometryDataPackages, display 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.HeLa.bam.chr14 Exports: RNAseqData.HeLa.bam.chr14_RUNNAMES, RNAseqData.HeLa.bam.chr14_BAMFILES Package: RNAseqData.HNRNPC.bam.chr14 Exports: RNAseqData.HNRNPC.bam.chr14_RUNNAMES, RNAseqData.HNRNPC.bam.chr14_BAMFILES Package: SNAGEEdata Exports: getCC Package: synapterdata Exports: getHDMSeFinalPeptide, getMSeFinalPeptide, getMSePep3D, loadMaster, getMaster, getFasta Package: TBX20BamSubset Exports: getBamFileList