# ChIPseeker for ChIP peak Annotation, Comparison, and Visualization

## Documentation for package ‘ChIPseeker’ version 1.49.0

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## Help Pages

. | .
.ChIPseekerEnv | env function for ChIPseeker
annotatePeak | annotatePeak
as.data.frame.csAnno | as.data.frame.csAnno
as.GRanges | as.GRanges
check_upstream_and_downstream | check upstream and downstream parameter
ChIPseekerCache | Name of the ChIPseeker cache environment (internal static variable)
combine_csAnno | combine_csAnno
covplot | covplot
csAnno-class | Class "csAnno" This class represents the output of ChIPseeker Annotation
downloadGEObedFiles | downloadGEObedFiles
downloadGSMbedFiles | downloadGSMbedFiles
dropAnno | dropAnno
enrichAnnoOverlap | enrichAnnoOverlap
enrichPeakOverlap | enrichPeakOverlap
getAnnoStat | getAnnoStat
getBioRegion | getBioRegion
getGeneAnno | getGeneAnno
getGenomicAnnotation | getGenomicAnnotation
getGEOgenomeVersion | getGEOgenomeVersion
getGEOInfo | getGEOInfo
getGEOspecies | getGEOspecies
getNearestFeatureIndicesAndDistances | getNearestFeatureIndicesAndDistances
getPromoters | getPromoters
getSampleFiles | getSampleFiles
getTagMatrix | getTagMatrix
getTagMatrix.binning.internal | getTagMatrix.binning.internal
getTagMatrix.internal | getTagMatrix.internal
getTagMatrix2 | getTagMatrix2
getTagMatrix2.binning.internal | internal function
getTagMatrix2.internal | getTagMatrix2.internal
gsminfo | Information Datasets
info | Information Datasets
makeBioRegionFromGranges | makeBioRegionFromGranges
make_label | make label for figures
overlap | overlap
peakHeatmap | peakHeatmap
peakHeatmap_multiple_Sets | peakHeatmap
peak_Profile_Heatmap | peak_Profile_Heatmap
plotAnnoBar | plotAnnoBar method generics
plotAnnoBar-method | Class "csAnno" This class represents the output of ChIPseeker Annotation
plotAnnoBar-method | plotAnnoBar method generics
plotAnnoBar.data.frame | plotAnnoBar.data.frame
plotAnnoPie | plotAnnoPie method generics
plotAnnoPie-method | Class "csAnno" This class represents the output of ChIPseeker Annotation
plotAnnoPie-method | plotAnnoPie method generics
plotAnnoPie.csAnno | plotAnnoPie
plotAvgProf | plotAvgProf
plotAvgProf.binning | plotAvgProf.binning
plotAvgProf2 | plotAvgProf
plotDistToTSS | plotDistToTSS method generics
plotDistToTSS-method | Class "csAnno" This class represents the output of ChIPseeker Annotation
plotDistToTSS-method | plotDistToTSS method generics
plotDistToTSS.data.frame | plotDistToTSS.data.frame
plotMultiProf | internal function for plotPeakProf_MultiWindows
plotMultiProf.binning | internal function
plotMultiProf.binning.internal | internal function
plotMultiProf.normal | internal function
plotMultiProf.normal.internal | internal function
plotPeakProf | plotPeakProf_MultiWindows
plotPeakProf2 | plotPeakProf2
plotPeakProf_MultiWindows | plotPeakProf_MultiWindows
readPeakFile | readPeakFile
seq2gene | seq2gene
show | show method
show-method | Class "csAnno" This class represents the output of ChIPseeker Annotation
show-method | show method
shuffle | shuffle
subset-method | Class "csAnno" This class represents the output of ChIPseeker Annotation
tagHeatmap | tagHeatmap
tagMatrixList | Information Datasets
ucsc_release | Information Datasets
upsetplot | upsetplot method
upsetplot-method | Class "csAnno" This class represents the output of ChIPseeker Annotation
vennpie | vennpie method generics
vennpie-method | Class "csAnno" This class represents the output of ChIPseeker Annotation
vennplot | vennplot
vennplot.peakfile | vennplot.peakfile