Files in ChIPpeakAnno

Batch annotation of the peaks identified from either ChIP-seq, ChIP-chip experiments or any experiments resulted in large number of chromosome ranges

README.md R/featureAlignedExtendSignal.R R/genomicElementUpSetR.R R/getEnrichedPATH.R R/annotatePeakInBatch.R R/ExonPlusUtr.human.GRCh37.R R/estFragmentLength.R R/downstreams.R R/mergePlusMinusPeaks.R R/countPatternInSeqs.R R/getGeneSeq.R R/TSS.human.GRCh38.R R/featureAlignedSignal.R R/hyperGtest.R R/preparePool.R R/IDRfilter.R R/permPool.R R/addGeneIDs.R R/TSS.mouse.NCBIM37.R R/wgEncodeTfbsV3.R R/bindist.R R/TSS.zebrafish.Zv8.R R/expandGR.R R/getAllPeakSequence.R R/metagene.R R/peakPermTest.R R/binOverFeature.R R/TSS.rat.RGSC3.4.R R/makeVennDiagram.R R/annoGR.R R/enrichedGO.R R/addMetadata.R R/findOverlappingPeaks.R R/assignChromosomeRegion.R R/estLibSize.R R/featureAlignedDistribution.R R/toGRanges.R R/tileGRanges.R R/randPeaks.R R/annotatedPeak.R R/findMotifsInPromoterSeqs.R R/TSS.mouse.GRCm38.R R/getAnnotation.R R/TSS.zebrafish.Zv9.R R/summarizeOverlapsByBins.R R/buildBindingDistribution.R R/ratio.zScore.R R/peaksNearBDP.R R/condenseMatrixByColnames.R R/HOT.spots.R R/TSS.rat.Rnor_5.0.R R/getEnrichedGO.R R/tileCount.R R/summarizePatternInPeaks.R R/egOrgMap.R R/addAncestors.R R/reCenterPeaks.R R/enrichmentPlot.R R/cntOverlaps.R R/bdp.R R/myPeakList.R R/convert2EntrezID.R R/findOverlapsOfPeaks.R R/write2FASTA.R R/Peaks.Ste12.R R/xget.R R/getGO.R R/findEnhancers.R R/getUniqueGOidCount.R R/getVennCounts.R R/pie1.R R/annoPeaks.R R/featureAlignedHeatmap.R R/TSS.human.NCBI36.R R/oligoSummary.R R/cumulativePercentage.R R/binOverRegions.R R/ChIPpeakAnno-deprecated.R R/TSS.human.GRCh37.R R/genomicElementDistribution.R R/ChIPpeakAnno.R R/translatePattern.R R/privateUtil.R R/binOverGene.R inst/doc/FAQs.Rmd inst/doc/ChIPpeakAnno.Rmd inst/doc/FAQs.R inst/doc/pipeline.R inst/doc/pipeline.Rmd inst/doc/ChIPpeakAnno.R inst/doc/quickStart.Rmd inst/doc/quickStart.R tests/runTests.R tests/testthat/test_downstreams.R tests/testthat/test_addMetadata.R tests/testthat/test_peaksNearBDP.R tests/testthat/test_getAllPeakSequence.R tests/testthat/test_reCenterPeaks.R tests/testthat/test_binOverRegions.R tests/testthat/test_feature.R tests/testthat/test_getVennCounts.R tests/testthat/test_findOverlapsOfPeaks.R tests/testthat/test_binOverFeature.R tests/testthat/test_annoPeaks.R tests/testthat/test_annotatePeakInBatch.R tests/testthat/test_getAnnotation.R tests/testthat/test_write2FASTA.R tests/testthat/test_bdp.R tests/testthat/test_filterByOverlaps.R tests/testthat/test_toGRanges.R tests/testthat/test_makeVennDiagram.R tests/testthat/test_addGeneIDs.R tests/testthat/test_binOverGene.R tests/testthat/test_assignChromosomeRegion.R tests/testthat/test_findEnhancers.R vignettes/FAQs.Rmd vignettes/ChIPpeakAnno.Rmd vignettes/pipeline.Rmd vignettes/quickStart.Rmd man/summarizeOverlapsByBins.Rd man/featureAlignedDistribution.Rd man/genomicElementUpSetR.Rd man/TSS.rat.RGSC3.4.Rd man/binOverRegions.Rd man/tileGRanges.Rd man/getAnnotation.Rd man/enrichmentPlot.Rd man/reCenterPeaks.Rd man/annotatePeakInBatch.Rd man/makeVennDiagram.Rd man/enrichedGO.Rd man/TSS.zebrafish.Zv8.Rd man/TSS.mouse.GRCm38.Rd man/annoPeaks.Rd man/annoGR.Rd man/myPeakList.Rd man/TSS.rat.Rnor_5.0.Rd man/addMetadata.Rd man/convert2EntrezID.Rd man/Peaks.Ste12.Replicate3.Rd man/peaksNearBDP.Rd man/TSS.human.NCBI36.Rd man/findOverlapsOfPeaks.Rd man/permPool.Rd man/preparePool.Rd man/peakPermTest.Rd man/write2FASTA.Rd man/bindist.Rd man/countPatternInSeqs.Rd man/ChIPpeakAnno-deprecated.Rd man/getEnrichedPATH.Rd man/condenseMatrixByColnames.Rd man/addAncestors.Rd man/assignChromosomeRegion.Rd man/estFragmentLength.Rd man/ExonPlusUtr.human.GRCh37.Rd man/getGeneSeq.Rd man/findEnhancers.Rd man/tileCount.Rd man/IDRfilter.Rd man/getVennCounts.Rd man/findMotifsInPromoterSeqs.Rd man/TSS.zebrafish.Zv9.Rd man/HOT.spots.Rd man/plotBinOverRegions.Rd man/pie1.Rd man/TxDb2GR.Rd man/wgEncodeTfbsV3.Rd man/getAllPeakSequence.Rd man/metagenePlot.Rd man/getEnrichedGO.Rd man/downstreams.Rd man/featureAlignedExtendSignal.Rd man/ChIPpeakAnno-package.Rd man/getUniqueGOidCount.Rd man/Peaks.Ste12.Replicate1.Rd man/TSS.mouse.NCBIM37.Rd man/TSS.human.GRCh38.Rd man/estLibSize.Rd man/bdp.Rd man/xget.Rd man/findOverlappingPeaks.Rd man/addGeneIDs.Rd man/Peaks.Ste12.Replicate2.Rd man/EnsDb2GR.Rd man/featureAlignedHeatmap.Rd man/oligoSummary.Rd man/TSS.human.GRCh37.Rd man/genomicElementDistribution.Rd man/toGRanges.Rd man/cntOverlaps.Rd man/cumulativePercentage.Rd man/translatePattern.Rd man/egOrgMap.Rd man/summarizePatternInPeaks.Rd man/annotatedPeak.Rd man/hyperGtest.Rd man/featureAlignedSignal.Rd man/mergePlusMinusPeaks.Rd man/getGO.Rd man/oligoFrequency.Rd man/binOverGene.Rd man/binOverFeature.Rd