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
