API for jianhong/ChIPpeakAnno
Batch annotation of the peaks identified from either ChIP-seq, ChIP-chip experiments, or any experiments that result in large number of genomic interval data
| Global functions | |
|---|---|
| $,bindist-method | Man page |
| $,permPool-method | Man page |
| $<-,bindist-method | Man page |
| $<-,permPool-method | Man page |
| .findKEGGRESTOrganismName | Source code |
| ChIPpeakAnno | Man page |
| ChIPpeakAnno-deprecated | Man page |
| ChIPpeakAnno-package | Man page |
| EnsDb2GR | Man page Source code |
| ExonPlusUtr.human.GRCh37 | Man page |
| HOT.spots | Man page |
| IDRfilter | Man page Source code |
| Peaks.Ste12.Replicate1 | Man page |
| Peaks.Ste12.Replicate2 | Man page |
| Peaks.Ste12.Replicate3 | Man page |
| TSS.human.GRCh37 | Man page |
| TSS.human.GRCh38 | Man page |
| TSS.human.NCBI36 | Man page |
| TSS.mouse.GRCm38 | Man page |
| TSS.mouse.NCBIM37 | Man page |
| TSS.rat.RGSC3.4 | Man page |
| TSS.rat.Rnor_5.0 | Man page |
| TSS.zebrafish.Zv8 | Man page |
| TSS.zebrafish.Zv9 | Man page |
| TxDb2GR | Man page Source code |
| addAncestors | Man page Source code |
| addGeneIDs | Man page Source code |
| addMetadata | Man page Source code |
| annoGR | Man page |
| annoGR,EnsDb-method | Man page |
| annoGR,GRanges-method | Man page |
| annoGR,TxDb-method | Man page |
| annoGR-class | Man page |
| annoPeaks | Man page Source code |
| annoScore | Source code |
| annotatePeakInBatch | Man page |
| annotatedPeak | Man page |
| assignChromosomeRegion | Man page Source code |
| bdp | Man page Source code |
| binOverFeature | Man page Source code |
| binOverGene | Man page Source code |
| binOverRegions | Man page Source code |
| bindist | Man page |
| bindist-class | Man page |
| bindist-method | Man page |
| binomEnrichment | Source code |
| buildBindingDistribution | Source code |
| cntOverlaps | Man page Source code |
| coerce | Man page |
| coerce,GRanges,annoGR-method | Man page |
| coerce,annoGR,GRanges-method | Man page |
| condenseMatrixByColnames | Man page Source code |
| convert2EntrezID | Man page Source code |
| countByOverlaps | Source code |
| countPatternInSeqs | Man page Source code |
| cumulativePercentage | Man page Source code |
| df2GRanges | Source code |
| downstreams | Man page Source code |
| egOrgMap | Man page Source code |
| enrichedGO | Man page |
| enrichmentPlot | Man page Source code |
| estFragmentLength | Man page Source code |
| estLibSize | Man page Source code |
| expandGR | Source code |
| expandPattern | Source code |
| expectMotifFrequency | Source code |
| featureAlignedDistribution | Man page Source code |
| featureAlignedExtendSignal | Man page Source code |
| featureAlignedHeatmap | Man page Source code |
| featureAlignedSignal | Man page Source code |
| filterByLevel | Source code |
| filterByOverlaps | Source code |
| findEnhancers | Man page Source code |
| findMotifsInPromoterSeqs | Man page Source code |
| findOverlappingPeaks | Man page Source code |
| findOverlappingPeaks-deprecated | Man page |
| findOverlaps1 | Source code |
| findOverlapsOfPeaks | Man page Source code |
| formatSeqnames | Source code |
| formatStrand | Source code |
| genomicElementDistribution | Man page Source code |
| genomicElementUpSetR | Man page Source code |
| getAllPeakSequence | Man page Source code |
| getAnnotation | Man page Source code |
| getEnrichedGO | Man page Source code |
| getEnrichedPATH | Man page Source code |
| getGO | Man page Source code |
| getGOLevel | Source code |
| getGeneSeq | Man page Source code |
| getPosInSeqs | Source code |
| getRelationship | Source code |
| getUniqueGOidCount | Man page Source code |
| getVennCounts | Man page Source code |
| hyperGtest | Man page Source code |
| info | Man page |
| info,annoGR-method | Man page |
| makeVennDiagram | Man page Source code |
| mergePlusMinusPeaks | Man page Source code |
| message4GTF | Source code |
| metagenePlot | Man page Source code |
| myPeakList | Man page |
| newAGR | Source code |
| oligoFrequency | Man page Source code |
| oligoSummary | Man page Source code |
| overlappingPeaks | Man page |
| overlappingPeaks-class | Man page |
| patternEnrichmentInPeak | Source code |
| peakPermTest | Man page Source code |
| peaks1 | Man page |
| peaks2 | Man page |
| peaks3 | Man page |
| peaksNearBDP | Man page Source code |
| permPool | Man page |
| permPool-class | Man page |
| permPool-method | Man page |
| permutationEnrichment | Source code |
| pie1 | Man page |
| plotBinOverRegions | Man page Source code |
| preparePool | Man page Source code |
| randPeaks | Source code |
| ratio.zScore | Source code |
| reCenterPeaks | Man page Source code |
| removeAncestor | Source code |
| removeLabelSubstring | Source code |
| runifGR | Source code |
| shortStrs | Source code |
| summarizeOverlapsByBins | Man page Source code |
| summarizePatternInPeaks | Man page Source code |
| swapList | Source code |
| switchColNames | Source code |
| tileCount | Man page Source code |
| tileGRanges | Man page Source code |
| toGRanges | Man page |
| toGRanges,EnsDb-method | Man page |
| toGRanges,TxDb-method | Man page |
| toGRanges,character-method | Man page |
| toGRanges,connection-method | Man page |
| toGRanges,data.frame-method | Man page |
| translatePattern | Man page Source code |
| trimPeakList | Source code |
| vennCounts | Source code |
| wgEncodeTfbsV3 | Man page |
| write2FASTA | Man page Source code |
| xget | Man page Source code |
