ChIPseeker for ChIP peak Annotation, Comparison, and Visualization

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Documentation for package ‘ChIPseeker’ version 1.49.1

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

Help Pages

ChIPseeker-package	ChIPseeker: ChIP peak Annotation, Comparison, and Visualization
.	.
.ChIPseekerEnv	Initialize and manage ChIPseeker cache environment
annotatePeak	Annotate peaks with genomic features
arrange.GRanges	Arrange (sort) GRanges objects using dplyr syntax
as.data.frame.csAnno	Convert csAnno object to data.frame
as.GRanges	Convert csAnno object to GRanges
ChIPseeker	ChIPseeker: ChIP peak Annotation, Comparison, and Visualization
combine_csAnno	Combine multiple csAnno objects
covplot	Plot peak coverage across chromosomes
csAnno-class	Class "csAnno"
downloadGEObedFiles	downloadGEObedFiles
downloadGSMbedFiles	downloadGSMbedFiles
dropAnno	dropAnno
enrichAnnoOverlap	Calculate overlap significance of ChIP experiments based on nearest gene annotation
enrichPeakOverlap	Calculate overlap significance of ChIP experiments based on genomic coordinates
filter.GRanges	Filter GRanges objects using dplyr syntax
getAnnoStat	Get annotation statistics from csAnno object
getBioRegion	Prepare a biological region of selected feature from TxDb
getGeneAnno	Get gene annotation from annotation database
getGEOgenomeVersion	getGEOgenomeVersion
getGEOInfo	getGEOInfo
getGEOspecies	getGEOspecies
getNearestFeatureIndicesAndDistances	Get index of nearest features to peaks and calculate distances
getPromoters	Prepare promoter regions from TxDb
getSampleFiles	Get sample peak files included in the package
getTagMatrix	Calculate tag matrix for peak coverage visualization
getTagMatrix.binning.internal	Calculate tag matrix using binning method (internal function)
gsminfo	Information Datasets
info	Information Datasets
makeBioRegionFromGranges	Make biological regions from user-provided GRanges object
mutate.GRanges	Mutate GRanges objects using dplyr syntax
overlap	Calculate overlap matrix for sets
peakHeatmap	Plot heatmap of peaks around genomic features
peakHeatmap_multiple_Sets	Plot heatmap of peaks aligned to multiple sets of regions
peak_Profile_Heatmap	Plot combined peak heatmap and average profile
plotAnnoBar	Plot bar chart of genomic annotation distribution
plotAnnoBar-method	Class "csAnno"
plotAnnoBar-method	Plot bar chart of genomic annotation distribution
plotAnnoBar.data.frame	plotAnnoBar.data.frame
plotAnnoPie	Plot pie chart of genomic annotation distribution
plotAnnoPie-method	Class "csAnno"
plotAnnoPie.csAnno	plotAnnoPie
plotAvgProf	plot the profile of peaks
plotAvgProf2	plotAvgProf2
plotDistToTSS	Plot feature distribution based on distances to TSS
plotDistToTSS-method	Class "csAnno"
plotDistToTSS-method	Plot feature distribution based on distances to TSS
plotDistToTSS.data.frame	Plot feature distribution based on distances to TSS
plotPeakProf	plotPeakProf_MultiWindows
plotPeakProf2	plotPeakProf2
readPeakFile	Read peak file and convert to GRanges or data.frame
rename.GRanges	Rename columns in GRanges objects using dplyr syntax
seq2gene	Annotate genomic regions to genes in many-to-many mapping
show-method	Class "csAnno"
shuffle	Shuffle peak positions across the genome
subset-method	Class "csAnno"
subset.csAnno	Subset csAnno object
tagHeatmap	tagHeatmap
tagMatrixList	Information Datasets
ucsc_release	Information Datasets
upsetplot-method	Class "csAnno"
upsetplot.csAnno	Create UpSet plot for genomic annotation combinations
vennpie	Create Venn pie chart for genomic annotation distribution
vennpie-method	Class "csAnno"
vennpie.csAnno	Create Venn pie chart for genomic annotation distribution
vennplot	Plot Venn diagram for overlapping sets
vennplot.peakfile	Plot Venn diagram for peak files