# ChIPseeker for ChIP peak Annotation, Comparison, and Visualization

## Documentation for package ‘ChIPseeker’ version 1.12.1

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

## Help Pages

ChIPseeker-package | ChIP-SEQ Annotation, Visualization and Comparison
. | .
annotatePeak | annotatePeak
as.data.frame.csAnno | as.data.frame.csAnno
as.GRanges | as.GRanges
ChIPseeker | ChIP-SEQ Annotation, Visualization and Comparison
covplot | covplot
csAnno-class | Class "csAnno" This class represents the output of ChIPseeker Annotation
downloadGEObedFiles | downloadGEObedFiles
downloadGSMbedFiles | downloadGSMbedFiles
dropAnno | dropAnno
enrichAnnoOverlap | enrichAnnoOverlap
enrichPeakOverlap | enrichPeakOverlap
getBioRegion | getBioRegion
getGeneAnno | getGeneAnno
getGenomicAnnotation | getGenomicAnnotation
getGEOgenomeVersion | getGEOgenomeVersion
getGEOInfo | getGEOInfo
getGEOspecies | getGEOspecies
getNearestFeatureIndicesAndDistances | getNearestFeatureIndicesAndDistances
getPromoters | getPromoters
getSampleFiles | getSampleFiles
getTagMatrix | getTagMatrix
gsminfo | Information Datasets
info | Information Datasets
overlap | overlap
peakHeatmap | peakHeatmap
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
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
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
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