Package: ChIPseeker 1.48.0

Guangchuang Yu

ChIPseeker: ChIPseeker for ChIP peak Annotation, Comparison, and Visualization

This package implements functions to retrieve the nearest genes around the peak, annotate genomic region of the peak, statstical methods for estimate the significance of overlap among ChIP peak data sets, and incorporate GEO database for user to compare the own dataset with those deposited in database. The comparison can be used to infer cooperative regulation and thus can be used to generate hypotheses. Several visualization functions are implemented to summarize the coverage of the peak experiment, average profile and heatmap of peaks binding to TSS regions, genomic annotation, distance to TSS, and overlap of peaks or genes.

Authors:Guangchuang Yu [aut, cre], Ming Li [ctb], Qianwen Wang [ctb], Yun Yan [ctb], Hervé Pagès [ctb], Michael Kluge [ctb], Thomas Schwarzl [ctb], Zhougeng Xu [ctb], Chun-Hui Gao [ctb]

ChIPseeker_1.48.0.tar.gz
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ChIPseeker_1.48.0.tgz(r-4.6-any)ChIPseeker_1.48.0.tgz(r-4.5-any)
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manual.pdf |manual.html✨
card.svg |card.png
ChIPseeker/json (API)
NEWS

# Install 'ChIPseeker' in R:
install.packages('ChIPseeker', repos = c('https://bioc-release.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/yulab-smu/chipseeker/issues

Datasets:

On BioConductor:ChIPseeker-1.49.0(bioc 3.24)ChIPseeker-1.48.0(bioc 3.23)

annotationchipseqsoftwarevisualizationmultiplecomparisonatac-seqchip-seqcomparisonepigeneticsepigenomics

13.26 score 256 stars 4 packages 2.7k scripts 5.0k downloads 161 mentions 42 exports 148 dependencies

Last updated from:6c4d5bcd1d (on RELEASE_3_23). Checks:1 ERROR, 9 OK. Indexed: no.

TargetResultTimeFilesSyslog
bioc-checksERROR346
linux-devel-x86_64OK649
source / vignettesOK825
linux-release-x86_64OK717
macos-release-arm64OK480
macos-oldrel-arm64OK452
windows-develOK521
windows-releaseOK562
windows-oldrelOK549
wasm-releaseOK340

Exports:.annotatePeakas.GRangescombine_csAnnocovplotdownloadGEObedFilesdownloadGSMbedFilesdropAnnoenrichAnnoOverlapenrichPeakOverlapgetAnnoStatgetBioRegiongetGEOgenomeVersiongetGEOInfogetGEOspeciesgetPromotersgetSampleFilesgetTagMatrixGRangesListmakeBioRegionFromGrangesoverlappeak_Profile_HeatmappeakHeatmappeakHeatmap_multiple_SetsplotAnnoBarplotAnnoPieplotAnnoPie.csAnnoplotAvgProfplotAvgProf2plotDistToTSSplotPeakProfplotPeakProf2readPeakFilerelseq2geneshowshuffletagHeatmapupsetplotvennpievennplotvennplot.peakfile

Dependencies:abindAnnotationDbiapeaplotaskpassbase64encBHBiobaseBiocGenericsBiocIOBiocParallelBiostringsbitbit64bitopsblobbootbslibcachemcaToolscigarillocliclustercodetoolscpp11crayoncurlDBIDelayedArraydigestDOSEdplyrenrichitenrichplotevaluatefarverfastmapfontawesomefontBitstreamVerafontLiberationfontquiverformatRfsfutile.loggerfutile.optionsgdtoolsgenericsGenomeInfoDbGenomicAlignmentsGenomicFeaturesGenomicRangesggforceggfunggiraphggnewscaleggplot2ggplotifyggrepelggtangleggtreeglueGO.dbGOSemSimgplotsgridGraphicsgtablegtoolshighrhtmltoolshtmlwidgetshttrigraphIRangesisobandjquerylibjsonliteKEGGRESTKernSmoothknitrlabelinglambda.rlatticelazyevallifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemimenlmeopensslpatchworkpillarpkgconfigplotrixplyrpngpolyclippurrrR6rappdirsRColorBrewerRcppRCurlreshape2restfulrRhtslibrjsonrlangrmarkdownRsamtoolsRSQLitertracklayerS4ArraysS4VectorsS7sassscalesscatterpieSeqinfosnowSparseArraystringistringrSummarizedExperimentsyssystemfontstibbletidydrtidyrtidyselecttidytreetinytextreeiotweenrTxDb.Hsapiens.UCSC.hg19.knownGeneUCSC.utilsutf8vctrsviridisLitewithrxfunXMLXVectoryamlyulab.utils

ChIPseeker: an R package for ChIP peak Annotation, Comparison and Visualization

Guangchuang Yu School of Basic Medical Sciences, Southern Medical University

Rendered fromChIPseeker.Rmdusingknitr::rmarkdownon Jun 02 2026.

Last update: 2024-10-06
Started: 2015-05-17

Readme and manuals

Help Manual

Help pageTopics
..
env function for ChIPseeker.ChIPseekerEnv
annotatePeakannotatePeak
as.data.frame.csAnnoas.data.frame.csAnno
as.GRangesas.GRanges
check upstream and downstream parametercheck_upstream_and_downstream
Name of the ChIPseeker cache environment (internal static variable)ChIPseekerCache
combine_csAnnocombine_csAnno
covplotcovplot
Class "csAnno" This class represents the output of ChIPseeker AnnotationcsAnno-class plotAnnoBar,csAnno-method plotAnnoPie,csAnno-method plotDistToTSS,csAnno-method show,csAnno-method subset,csAnno-method upsetplot,csAnno-method vennpie,csAnno-method
downloadGEObedFilesdownloadGEObedFiles
downloadGSMbedFilesdownloadGSMbedFiles
dropAnnodropAnno
enrichAnnoOverlapenrichAnnoOverlap
enrichPeakOverlapenrichPeakOverlap
getAnnoStatgetAnnoStat
getBioRegiongetBioRegion
getGeneAnnogetGeneAnno
getGenomicAnnotationgetGenomicAnnotation
getGEOgenomeVersiongetGEOgenomeVersion
getGEOInfogetGEOInfo
getGEOspeciesgetGEOspecies
getNearestFeatureIndicesAndDistancesgetNearestFeatureIndicesAndDistances
getPromotersgetPromoters
getSampleFilesgetSampleFiles
getTagMatrixgetTagMatrix
getTagMatrix.binning.internalgetTagMatrix.binning.internal
getTagMatrix.internalgetTagMatrix.internal
getTagMatrix2getTagMatrix2
internal functiongetTagMatrix2.binning.internal
getTagMatrix2.internalgetTagMatrix2.internal
Information Datasetsgsminfo info tagMatrixList ucsc_release
make label for figuresmake_label
makeBioRegionFromGrangesmakeBioRegionFromGranges
overlapoverlap
peak_Profile_Heatmappeak_Profile_Heatmap
peakHeatmappeakHeatmap
peakHeatmappeakHeatmap_multiple_Sets
plotAnnoBar method genericsplotAnnoBar plotAnnoBar,csAnno,ANY-method plotAnnoBar,list-method
plotAnnoBar.data.frameplotAnnoBar.data.frame
plotAnnoPie method genericsplotAnnoPie plotAnnoPie,csAnno,ANY-method
plotAnnoPieplotAnnoPie.csAnno
plotAvgProfplotAvgProf
plotAvgProf.binningplotAvgProf.binning
plotAvgProfplotAvgProf2
plotDistToTSS method genericsplotDistToTSS plotDistToTSS,csAnno,ANY-method plotDistToTSS,list-method
plotDistToTSS.data.frameplotDistToTSS.data.frame
internal function for plotPeakProf_MultiWindowsplotMultiProf
internal functionplotMultiProf.binning
internal functionplotMultiProf.binning.internal
internal functionplotMultiProf.normal
internal functionplotMultiProf.normal.internal
plotPeakProf_MultiWindowsplotPeakProf
plotPeakProf_MultiWindowsplotPeakProf_MultiWindows
plotPeakProf2plotPeakProf2
readPeakFilereadPeakFile
seq2geneseq2gene
show methodshow show,csAnno,ANY-method
shuffleshuffle
tagHeatmaptagHeatmap
upsetplot methodupsetplot
vennpie method genericsvennpie
vennplotvennplot
vennplot.peakfilevennplot.peakfile