# Comparison, Benchmarking & QC of Epigenomic Datasets

## Documentation for package ‘EpiCompare’ version 1.2.0

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

## Help Pages

bpplapply | Wrapper for bplapply
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
compute_consensus_peaks | Compute consensus peaks
compute_corr | Compute correlation matrix
encode_H3K27ac | Example ChIP-seq peak file
EpiCompare | Compare epigenomic datasets
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
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
rebin_peaks | Rebin peaks
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