API for DiffBind
Differential Binding Analysis of ChIP-Seq Peak Data

Global functions
DBA Man page
DBA_ALL_ATTRIBUTES Man page
DBA_ALL_BLOCK Man page
DBA_ALL_METHODS Man page
DBA_ALL_METHODS_BLOCK Man page
DBA_CALLER Man page
DBA_CONDITION Man page
DBA_CONSENSUS Man page
DBA_CONTROL Man page
DBA_COR Man page
DBA_DATA_DBAOBJECT Man page
DBA_DATA_FRAME Man page
DBA_DATA_GRANGES Man page
DBA_DATA_RANGEDDATA Man page
DBA_DATA_SUMMARIZED_EXPERIMENT Man page
DBA_DESEQ Man page
DBA_DESEQ2 Man page
DBA_DESEQ2_BLOCK Man page
DBA_DESEQ_BLOCK Man page
DBA_DESEQ_CLASSIC Man page
DBA_DESEQ_GLM Man page
DBA_EDGER Man page
DBA_EDGER_BLOCK Man page
DBA_EDGER_CLASSIC Man page
DBA_EDGER_GLM Man page
DBA_FACTOR Man page
DBA_FRIP Man page
DBA_GROUP Man page
DBA_ID Man page
DBA_INALL Man page
DBA_INTERVALS Man page
DBA_OLAP Man page
DBA_OLAP_ALL Man page
DBA_OLAP_PEAKS Man page
DBA_OLAP_RATE Man page
DBA_READS_BAM Man page
DBA_READS_BED Man page
DBA_READS_DEFAULT Man page
DBA_REPLICATE Man page
DBA_SCORE_READS Man page
DBA_SCORE_READS_FOLD Man page
DBA_SCORE_READS_MINUS Man page
DBA_SCORE_RPKM Man page
DBA_SCORE_RPKM_FOLD Man page
DBA_SCORE_SUMMIT Man page
DBA_SCORE_SUMMIT_ADJ Man page
DBA_SCORE_SUMMIT_POS Man page
DBA_SCORE_TMM_MINUS_EFFECTIVE Man page
DBA_SCORE_TMM_MINUS_EFFECTIVE_CPM Man page
DBA_SCORE_TMM_MINUS_FULL Man page
DBA_SCORE_TMM_MINUS_FULL_CPM Man page
DBA_SCORE_TMM_READS_EFFECTIVE Man page
DBA_SCORE_TMM_READS_EFFECTIVE_CPM Man page
DBA_SCORE_TMM_READS_FULL Man page
DBA_SCORE_TMM_READS_FULL_CPM Man page
DBA_TISSUE Man page
DBA_TREATMENT Man page
DiffBind Man page
DiffBind-package Man page
checkQCobj Source code
checkinvalid Source code
cpp_count_reads Source code
dba Man page Source code
dba.analyze Man page Source code
dba.biocparallel.addjob Source code
dba.biocparallel.init Source code
dba.biocparallel.lapply Source code
dba.biocparallel.params Source code
dba.biocparallel.wait4jobs Source code
dba.contrast Man page Source code
dba.count Man page Source code
dba.load Man page Source code
dba.mask Man page Source code
dba.multicore.addjob Source code
dba.multicore.init Source code
dba.multicore.lapply Source code
dba.multicore.params Source code
dba.multicore.wait4jobs Source code
dba.overlap Man page Source code
dba.parallel Source code
dba.parallel.addjob Source code
dba.parallel.init Source code
dba.parallel.lapply Source code
dba.parallel.params Source code
dba.parallel.wait4jobs Source code
dba.peakset Man page Source code
dba.plotBox Man page Source code
dba.plotClust Source code
dba.plotHeatmap Man page Source code
dba.plotMA Man page Source code
dba.plotPCA Man page Source code
dba.plotVenn Man page Source code
dba.plotVolcano Man page Source code
dba.report Man page Source code
dba.save Man page Source code
dba.show Man page Source code
fdebug Source code
hasHeader Source code
heatmap.3 Source code
makepv Source code
mergePeaks Source code
mergeScores Source code
peakOrder Source code
plot.DBA Man page Source code
print.DBA Man page Source code
pv.BlockList Source code
pv.CalledMasks Source code
pv.DBA Source code
pv.DBA2SummarizedExperiment Source code
pv.DBAplotMA Source code
pv.DBAplotVolcano Source code
pv.DBAreport Source code
pv.DESeq Source code
pv.DESeq2 Source code
pv.DESeq2_parallel Source code
pv.DESeq_parallel Source code
pv.DEedgeR Source code
pv.DEedgeR_parallel Source code
pv.DEinit Source code
pv.DataType2Peaks Source code
pv.Recenter Source code
pv.Signal2Noise Source code
pv.activefun Source code
pv.addContrast Source code
pv.add_consensus Source code
pv.addrow Source code
pv.addstr Source code
pv.allDESeq Source code
pv.allDESeq2 Source code
pv.allDEedgeR Source code
pv.allSame Source code
pv.analysis Source code
pv.assaysFromPeaks Source code
pv.attname Source code
pv.attributePCA Source code
pv.attributematrix Source code
pv.bayes Source code
pv.blockFactors Source code
pv.box Source code
pv.catstr Source code
pv.check Source code
pv.check1 Source code
pv.checkBlock Source code
pv.checkCounts Source code
pv.checkExists Source code
pv.checkValue Source code
pv.colorv Source code
pv.consensus Source code
pv.consensusSets Source code
pv.contrast Source code
pv.contrast2 Source code
pv.contrast3 Source code
pv.contrast4 Source code
pv.contrastDups Source code
pv.contrastPairs Source code
pv.controlID Source code
pv.countOverlap Source code
pv.counts Source code
pv.csv Source code
pv.defaultScoreCol Source code
pv.design Source code
pv.doPCAplot Source code
pv.doResults Source code
pv.do_getCounts Source code
pv.do_peaks2bed Source code
pv.domean Source code
pv.dval Source code
pv.filterRate Source code
pv.gc Source code
pv.getContrasts Source code
pv.getCounts Source code
pv.getCountsLowMem Source code
pv.getMethod Source code
pv.getOverlapData Source code
pv.getPlotData Source code
pv.get_reads Source code
pv.get_scores Source code
pv.getoneorNA Source code
pv.getsites Source code
pv.howmany Source code
pv.isConsensus Source code
pv.list Source code
pv.listContrasts Source code
pv.listadd Source code
pv.listaddto Source code
pv.load Source code
pv.macs Source code
pv.mask Source code
pv.matchingSamples Source code
pv.merge Source code
pv.minOverlap Source code
pv.model Source code
pv.morethanone Source code
pv.namestrings Source code
pv.nodup Source code
pv.normFactors Source code
pv.normTMM Source code
pv.normalize Source code
pv.nums2labels Source code
pv.occ2matrix Source code
pv.occupancy Source code
pv.orderfacs Source code
pv.overlap Source code
pv.overlapRate Source code
pv.overlapToLabels Source code
pv.overlaps Source code
pv.pairs Source code
pv.pcmask Source code
pv.peaks2DataType Source code
pv.peakset Source code
pv.peaksetCounts Source code
pv.peakset_all Source code
pv.peaksort Source code
pv.plotBoxplot Source code
pv.plotClust Source code
pv.plotHeatmap Source code
pv.plotPCA Source code
pv.plotVenn Source code
pv.readPeaks Source code
pv.readbed Source code
pv.removeComp Source code
pv.reorderM Source code
pv.resetCounts Source code
pv.resultsDBA Source code
pv.save Source code
pv.setMask Source code
pv.setScore Source code
pv.sicer Source code
pv.sort Source code
pv.sourcedata Source code
pv.stripDBA Source code
pv.stripDESeq1 Source code
pv.stripDESeq2 Source code
pv.stripEdgeR Source code
pv.stripEdgeRGLM Source code
pv.stripEdgeRLRT Source code
pv.swembl Source code
pv.tpic Source code
pv.vectors Source code
pv.venn2 Source code Source code
pv.venn3 Source code Source code
pv.venn4 Source code
pv.version Source code
pv.whichCalled Source code
pv.whichPeaksets Source code
pv.whichSites Source code
pv.writePeakset Source code
stripSpaces Source code
summary.DBA Man page Source code
tamoxifen Man page
tamoxifen_analysis Man page
tamoxifen_counts Man page
tamoxifen_peaks Man page
DiffBind documentation built on Dec. 17, 2017, 10:01 a.m.