API for DiffBind
Differential Binding Analysis of ChIP-Seq Peak Data
| Global functions | |
|---|---|
| .onAttach | Source code |
| 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_BLACKLIST | Man page |
| DBA_BLACKLISTED_PEAKS | Man page |
| DBA_BLACKLIST_CE10 | Man page |
| DBA_BLACKLIST_CE11 | Man page |
| DBA_BLACKLIST_DM3 | Man page |
| DBA_BLACKLIST_DM6 | Man page |
| DBA_BLACKLIST_GRCH37 | Man page |
| DBA_BLACKLIST_GRCH38 | Man page |
| DBA_BLACKLIST_HG19 | Man page |
| DBA_BLACKLIST_HG38 | Man page |
| DBA_BLACKLIST_MM10 | Man page |
| DBA_BLACKLIST_MM9 | 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_DESEQ2 | Man page |
| DBA_DESEQ2_BLOCK | Man page |
| DBA_EDGER | Man page |
| DBA_EDGER_BLOCK | Man page |
| DBA_EDGER_GLM | Man page |
| DBA_FACTOR | Man page |
| DBA_FRIP | Man page |
| DBA_GREYLIST | Man page |
| DBA_GROUP | Man page |
| DBA_ID | Man page |
| DBA_INALL | Man page |
| DBA_INTERVALS | Man page |
| DBA_LIBSIZE_BACKGROUND | Man page |
| DBA_LIBSIZE_DEFAULT | Man page |
| DBA_LIBSIZE_FULL | Man page |
| DBA_LIBSIZE_PEAKREADS | Man page |
| DBA_LIBSIZE_USER | Man page |
| DBA_NORM_DEFAULT | Man page |
| DBA_NORM_LIB | Man page |
| DBA_NORM_NATIVE | Man page |
| DBA_NORM_OFFSETS | Man page |
| DBA_NORM_OFFSETS_ADJUST | Man page |
| DBA_NORM_RLE | Man page |
| DBA_NORM_SPIKEIN | Man page |
| DBA_NORM_TMM | Man page |
| DBA_NORM_USER | Man page |
| DBA_OFFSETS_LOESS | Man page |
| DBA_OFFSETS_USER | Man page |
| DBA_OLAP | Man page |
| DBA_OLAP_ALL | Man page |
| DBA_OLAP_PEAKS | Man page |
| DBA_OLAP_RATE | Man page |
| DBA_READS | Man page |
| DBA_READS_BAM | Man page |
| DBA_READS_BED | Man page |
| DBA_READS_DEFAULT | Man page |
| DBA_REPLICATE | Man page |
| DBA_SCORE_CONTROL_READS | Man page |
| DBA_SCORE_NORMALIZED | Man page |
| DBA_SCORE_READS | Man page |
| DBA_SCORE_READS_EFFECTIVE | Man page |
| DBA_SCORE_READS_FOLD | Man page |
| DBA_SCORE_READS_FULL | Man page |
| DBA_SCORE_READS_MINUS | Man page |
| DBA_SCORE_READS_MINUS_EFFECTIVE | Man page |
| DBA_SCORE_READS_MINUS_FULL | Man page |
| DBA_SCORE_RPKM | Man page |
| DBA_SCORE_RPKM_FOLD | Man page |
| DBA_SCORE_RPKM_MINUS | 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 |
| DiffBind3 | Man page |
| checkQCobj | 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.blacklist | Man page 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.normalize | Man page 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.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 |
| 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.BamFile | Source code |
| pv.BlockList | Source code |
| pv.CalledMasks | Source code |
| pv.CheckReleveledContrasts | Source code |
| pv.DBA | Source code |
| pv.DBA2SummarizedExperiment | Source code |
| pv.DBAplotMA | Source code |
| pv.DBAplotVolcano | Source code |
| pv.DBAreport | Source code |
| pv.DESeq2 | Source code |
| pv.DESeq2Contrast | Source code |
| pv.DESeq2ResultsNames | Source code |
| pv.DESeq2_parallel | Source code |
| pv.DESeq2design | Source code |
| pv.DEedgeR | Source code |
| pv.DEedgeR_parallel | Source code |
| pv.DEinit | Source code |
| pv.DEinitDESeq2 | Source code |
| pv.DEinitedgeR | Source code |
| pv.DataType2Peaks | Source code |
| pv.Recenter | Source code |
| pv.ResetScores | 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.allDESeq2 | Source code |
| pv.allDEedgeR | Source code |
| pv.allSame | Source code |
| pv.analysis | Source code |
| pv.applyBlacklist | Source code |
| pv.assaysFromPeaks | Source code |
| pv.attname | Source code |
| pv.attributePCA | Source code |
| pv.attributematrix | Source code |
| pv.bayes | Source code |
| pv.blacklist | 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.checkConsensusRows | Source code |
| pv.checkContrast | Source code |
| pv.checkContrastOrder | Source code |
| pv.checkCounts | Source code |
| pv.checkDesign | Source code |
| pv.checkExists | Source code |
| pv.checkIntercept | Source code |
| pv.checkValue | Source code |
| pv.colorv | Source code |
| pv.compareDesigns | 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.contrastBlocks | Source code |
| pv.contrastCoeffs | Source code |
| pv.contrastDesign | Source code |
| pv.contrastDups | Source code |
| pv.contrastGroups | Source code |
| pv.contrastPairs | Source code |
| pv.contrastSDBs | Source code |
| pv.contrastTypes | Source code |
| pv.controlID | Source code |
| pv.countGreylist | Source code |
| pv.countOverlap | Source code |
| pv.counts | Source code |
| pv.countsMA | Source code |
| pv.csv | Source code |
| pv.defaultScoreCol | Source code |
| pv.design | Source code |
| pv.designAnalysis | Source code |
| pv.designAnalysis_parallel | Source code |
| pv.doBlacklist | Source code |
| pv.doFilter | Source code |
| pv.doPCAplot | Source code |
| pv.doRenormalize | Source code |
| pv.doResetScore | Source code |
| pv.doResults | Source code |
| pv.doSetScore | Source code |
| pv.do_getCounts | Source code |
| pv.do_peaks2bed | Source code |
| pv.domean | Source code |
| pv.dval | Source code |
| pv.edgeRContrast | Source code |
| pv.edgeRCounts | Source code |
| pv.edgeRdesign | Source code |
| pv.edgeRdesign.matrix | Source code |
| pv.edgeRtoDESeq2norm | Source code |
| pv.filterRate | Source code |
| pv.formatNorm | Source code |
| pv.gc | Source code |
| pv.generateDesignFromContrasts | Source code |
| pv.generateSimpleDesign | Source code |
| pv.genome | Source code |
| pv.genomes | Source code |
| pv.getBackground | Source code |
| pv.getCoef | Source code |
| pv.getCoeffs | Source code |
| pv.getContrastString | Source code |
| pv.getContrasts | Source code |
| pv.getCounts | Source code |
| pv.getCountsLowMem | Source code |
| pv.getMeta | Source code |
| pv.getMethod | Source code |
| pv.getNorm | Source code |
| pv.getOverlapData | Source code |
| pv.getPlotData | Source code |
| pv.getPlotDataComplexContrast | Source code |
| pv.getSamplesForFactorVal | Source code |
| pv.get_reads | Source code |
| pv.get_scores | Source code |
| pv.getoneorNA | Source code |
| pv.getsites | Source code |
| pv.greylist | Source code |
| pv.howmany | Source code |
| pv.infToNA | Source code |
| pv.isConsensus | Source code |
| pv.isDesign | Source code |
| pv.keepMeta | Source code |
| pv.list | Source code |
| pv.listContrasts | Source code |
| pv.listadd | Source code |
| pv.listaddto | Source code |
| pv.load | Source code |
| pv.loadPre3 | Source code |
| pv.macs | Source code |
| pv.makeGreylist | Source code |
| pv.makeGreylists | Source code |
| pv.makeProd1 | Source code |
| pv.mask | Source code |
| pv.matchCoefs | Source code |
| pv.matchingSamples | Source code |
| pv.merge | Source code |
| pv.mergeGreyLists | Source code |
| pv.minOverlap | Source code |
| pv.model | Source code |
| pv.morethanone | Source code |
| pv.namestrings | Source code |
| pv.noControls | Source code |
| pv.nodup | Source code |
| pv.normFactors | Source code |
| pv.normLibsize | Source code |
| pv.normTMM | Source code |
| pv.normalize | Source code |
| pv.normalizeOffsets | Source code |
| pv.normalizeRetrieve | Source code |
| pv.normalizeScores | Source code |
| pv.normfacsLIB | Source code |
| pv.normfacsRLE | Source code |
| pv.normfacsTMM | Source code |
| pv.nums2labels | Source code |
| pv.occ2matrix | Source code |
| pv.occupancy | Source code |
| pv.offsetsAdjust | Source code |
| pv.orderMetaFacs | 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.parallelFactor | 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.reNormalize | Source code |
| pv.readParams | Source code |
| pv.readPeaks | Source code |
| pv.readbed | Source code |
| pv.readsInPeaks | Source code |
| pv.removeBlacklistedPeaks | Source code |
| pv.removeResults | Source code |
| pv.reorderM | Source code |
| pv.resetCounts | Source code |
| pv.resultsDBA | Source code |
| pv.save | Source code |
| pv.setMask | Source code |
| pv.setNorm | Source code |
| pv.setScore | Source code |
| pv.sicer | Source code |
| pv.sort | Source code |
| pv.stripDBA | 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 |
| pv.venn3 | 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.greylist | Man page |
| tamoxifen_analysis | Man page |
| tamoxifen_counts | Man page |
| tamoxifen_greylist | Man page |
| tamoxifen_peaks | Man page |
