.                       .
.ChIPseekerEnv          Initialize and manage ChIPseeker cache
                        environment
ChIPseeker-package      ChIPseeker: ChIP peak Annotation, Comparison,
                        and Visualization
annotatePeak            Annotate peaks with genomic features
arrange.GRanges         Arrange (sort) GRanges objects using dplyr
                        syntax
as.GRanges              Convert csAnno object to GRanges
as.data.frame.csAnno    Convert csAnno object to data.frame
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
getGEOInfo              getGEOInfo
getGEOgenomeVersion     getGEOgenomeVersion
getGEOspecies           getGEOspecies
getGeneAnno             Get gene annotation from annotation database
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)
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.data.frame
                        plotAnnoBar.data.frame
plotAnnoPie             Plot pie chart of genomic annotation
                        distribution
plotAnnoPie.csAnno      plotAnnoPie
plotAvgProf             plot the profile of peaks
plotAvgProf2            plotAvgProf2
plotDistToTSS           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
shuffle                 Shuffle peak positions across the genome
subset.csAnno           Subset csAnno object
tagHeatmap              tagHeatmap
upsetplot.csAnno        Create UpSet plot for genomic annotation
                        combinations
vennpie                 Create Venn pie chart for genomic annotation
                        distribution
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
