Package: cgdv17 Exports: getRVS, getrd, countVariants, variantNames, padToReference ExportMethods: show, sampleNames, variantGRanges ExportClasses: raggedVariantSet Package: chipenrich.data ExportClasses: GeneSet, LocusDefinition Package: curatedBreastData Exports: processExpressionSetList, processExpressionSet, filterAndImputeSamples, collapseDupProbes, removeDuplicatedPatients, filterGenesByVariance Package: DAPARdata Exports: DAPARdata 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: 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: 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.synergyShadow, Fletcher2013pipeline.consensusnet, Fletcher2013pipeline.enrichmap, Fletcher2013gsea.regulons Package: furrowSeg Exports: area2px, constructBox, identifyFurrowPosition, identifyTimeMinArea, isOdd, isolateBoxCells, makeOdd, microns2px, plotFeatureEvolution, px2area, px2microns, segmentFurrowAllStacks Package: geuvStore Exports: partialRegistry, partialIds, makeGeuvStore Package: geuvStore2 Exports: makeGeuvStore2, g17transRegistry, g18transRegistry 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: 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: 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, 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: 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: msqc1 ExportClasses: msqc1 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: PGPC Exports: getFeaturesAllSpots, getInteractions, segmentAllSpots, segmentXman, summarizeWellsExtended Package: pRolocdata Exports: pRolocdata, pRolocmetadata, print.pRolocmetadata Package: RforProteomics Exports: getPXD000001mzXML, getPXD000001mzTab, getPXD000001mzData, getThermoHelaPRTC, downloadData, RforProteomics, RProtVis, RProtViz, proteomicsPackages, massSpectrometryPackages, massSpectrometryDataPackages, display, shinyMA 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: SNAGEEdata Exports: getCC Package: synapterdata Exports: getHDMSeFinalPeptide, getMSeFinalPeptide, getMSePep3D, loadMaster, getMaster, getFasta Package: systemPipeRdata Exports: pathList, genWorkenvir Package: TBX20BamSubset Exports: getBamFileList Package: TimerQuant Exports: signal, fitCV, genRatioHeatmap, genTimeSteadyStateHeatmap, getBreaks10, getSpacedSeq, plotPrimordiumProfile, ratioSteadyState, ratioTimeDependent, simulatedSignal, simulatedSignalN, simulatedRatio, tss, x0ss, x1, x1ss, x1fretFP1, x1fretFP1ss, runChooseFP2App, runTimerModellingApp