Files in 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

.gitignore

DESCRIPTION

NAMESPACE

NEWS

R/ChIPpeakAnno-deprecated.R R/ChIPpeakAnno.R R/ExonPlusUtr.human.GRCh37.R R/HOT.spots.R R/IDRfilter.R R/Peaks.Ste12.R R/TSS.human.GRCh37.R R/TSS.human.GRCh38.R R/TSS.human.NCBI36.R R/TSS.mouse.GRCm38.R R/TSS.mouse.NCBIM37.R R/TSS.rat.RGSC3.4.R R/TSS.rat.Rnor_5.0.R R/TSS.zebrafish.Zv8.R R/TSS.zebrafish.Zv9.R R/addAncestors.R R/addGeneIDs.R R/addMetadata.R R/annoGR.R R/annoPeaks.R R/annotatePeakInBatch.R R/annotatedPeak.R R/assignChromosomeRegion.R R/bdp.R R/binOverFeature.R R/binOverGene.R R/binOverRegions.R R/bindist.R R/buildBindingDistribution.R R/cntOverlaps.R R/condenseMatrixByColnames.R R/convert2EntrezID.R R/countPatternInSeqs.R R/cumulativePercentage.R R/downstreams.R R/egOrgMap.R R/enrichedGO.R R/enrichmentPlot.R R/estFragmentLength.R R/estLibSize.R R/expandGR.R R/featureAlignedDistribution.R R/featureAlignedExtendSignal.R R/featureAlignedHeatmap.R R/featureAlignedSignal.R R/findEnhancers.R R/findMotifsInPromoterSeqs.R R/findOverlappingPeaks.R R/findOverlapsOfPeaks.R R/genomicElementDistribution.R R/genomicElementUpSetR.R R/getAllPeakSequence.R R/getAnnotation.R R/getEnrichedGO.R R/getEnrichedPATH.R R/getGO.R R/getGeneSeq.R R/getUniqueGOidCount.R R/getVennCounts.R R/globalVariables.R R/hyperGtest.R R/makeVennDiagram.R R/mergePlusMinusPeaks.R R/metagene.R R/myPeakList.R R/oligoSummary.R R/peakPermTest.R R/peaks1.R R/peaks2.R R/peaks3.R R/peaksNearBDP.R R/permPool.R R/pie1.R R/preparePool.R R/privateUtil.R R/randPeaks.R R/ratio.zScore.R R/reCenterPeaks.R R/summarizeOverlapsByBins.R R/summarizePatternInPeaks.R R/tileCount.R R/tileGRanges.R R/toGRanges.R R/translatePattern.R R/wgEncodeTfbsV3.R R/write2FASTA.R R/xget.R README.md

data/ExonPlusUtr.human.GRCh37.rda

data/HOT.spots.rda

data/Peaks.Ste12.Replicate1.rda

data/Peaks.Ste12.Replicate2.rda

data/Peaks.Ste12.Replicate3.rda

data/TSS.human.GRCh37.rda

data/TSS.human.GRCh38.rda

data/TSS.human.NCBI36.rda

data/TSS.mouse.GRCm38.rda

data/TSS.mouse.NCBIM37.rda

data/TSS.rat.RGSC3.4.rda

data/TSS.rat.Rnor_5.0.rda

data/TSS.zebrafish.Zv8.rda

data/TSS.zebrafish.Zv9.rda

data/annotatedPeak.rda

data/enrichedGO.rda

data/myPeakList.rda

data/peaks1.rda

data/peaks2.rda

data/peaks3.rda

data/wgEncodeTfbsV3.rda

inst/CITATION

inst/extdata/GFF_peaks.gff

inst/extdata/GFF_peaks_hg38.bed

inst/extdata/GFF_peaks_hg38.gff

inst/extdata/GSM700906_AA86_vs_INPUT_WS170.bed

inst/extdata/GSM700907_DAF-12_TAP_vs_INPUT_#1_WS170.bed

inst/extdata/GSM700908_DAF-12_TAP_vs_INPUT_#2_WS170.bed

inst/extdata/GSM700909_DAF-12_TAP_vs_INPUT_#3_WS170.bed

inst/extdata/MACS2_peaks.xls

inst/extdata/MACS_output.bed

inst/extdata/MACS_output_hg38.bed

inst/extdata/MACS_peaks.xls

inst/extdata/TAF.bigWig

inst/extdata/TAF.broadPeak

inst/extdata/Tead4.bigWig

inst/extdata/Tead4.broadPeak

inst/extdata/WS220.bed

inst/extdata/YY1.bigWig

inst/extdata/YY1.broadPeak

inst/extdata/annoFeatureCentric1.png

inst/extdata/annoFeatureCentric1.svg

inst/extdata/annoFeatureCentric2.png

inst/extdata/annoFeatureCentric2.svg

inst/extdata/annoFeatureCentric3.png

inst/extdata/annoFeatureCentric3.svg

inst/extdata/annoPeakCentric.png

inst/extdata/annoPeakCentric.svg

inst/extdata/annotatedPeaks.2.10.0.rds

inst/extdata/cvglist.rds

inst/extdata/dataFlow.png

inst/extdata/dataFlow.svg

inst/extdata/examplePattern.fa

inst/extdata/gadem.rda

inst/extdata/guide-seq-peaks.txt

inst/extdata/motifAP1.fa

inst/extdata/motifIRF4.fa

inst/extdata/peaks.csv

inst/extdata/peaks.narrowPeak

inst/extdata/peaks_hg19.bed

inst/extdata/permTest1.png

inst/extdata/permTest2.png

inst/extdata/permTest3.png

inst/extdata/ref.gtf

inst/extdata/test.bed

inst/extdata/wgEncodeUmassDekker5CGm12878PkV2.bed.gz

vignettes/bibliography.bib

jianhong/ChIPpeakAnno documentation built on Nov. 1, 2024, 8:55 a.m.

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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

Files in 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

R Package Documentation

Browse R Packages

We want your feedback!

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

Files in 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

R Package Documentation

Browse R Packages

We want your feedback!

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

Files in 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