Function reference • EpiCompare

All functions
`CnR_H3K27ac`	Example CUT&Run peak file
`CnR_H3K27ac_picard`	Example Picard duplication metrics file 2
`CnT_H3K27ac`	Example CUT&Tag peak file
`CnT_H3K27ac_picard`	Example Picard duplication metrics file 1
`EpiCompare()`	Compare epigenomic datasets
`bpplapply()`	Wrapper for bplapply
`check_workers()`	Check workers
`compute_consensus_peaks()`	Compute consensus peaks
`compute_corr()`	Compute correlation matrix
`download_button()`	Download local file
`encode_H3K27ac`	Example ChIP-seq peak file
`fragment_info()`	Summary on fragments
`gather_files()`	Gather files
`group_files()`	Group files
`hg19_blacklist`	Human genome hg19 blacklisted regions
`hg38_blacklist`	Human genome hg38 blacklisted regions
`liftover_grlist()`	Liftover peak list
`mm10_blacklist`	Mouse genome mm10 blacklisted regions
`mm9_blacklist`	Mouse genome mm9 blacklisted regions
`overlap_heatmap()`	Generate heatmap of percentage overlap
`overlap_percent()`	Calculate percentage of overlapping peaks
`overlap_stat_plot()`	Statistical significance of overlapping peaks
`overlap_upset_plot()`	Generate Upset plot for overlapping peaks
`peak_info()`	Summary of Peak Information
`plot_ChIPseeker_annotation()`	Create ChIPseeker annotation plot
`plot_chromHMM()`	Plot ChromHMM heatmap
`plot_corr()`	Plot correlation of peak files
`plot_enrichment()`	Generate enrichment analysis plots
`plot_precision_recall()`	Plot precision-recall curves
`precision_recall()`	Compute precision-recall
`predict_precision_recall()`	Predict precision-recall
`rebin_peaks()`	Rebin peaks
`report_command()`	Report command
`report_header()`	Report header
`tidy_peakfile()`	Tidy peakfiles in GRanges
`translate_genome()`	Translate genome
`tss_plot()`	Read count frequency around TSS
`width_boxplot()`	Peak width boxplot
`write_example_peaks()`	Write example peaks

Reference

All functions