Comparison, Benchmarking & QC of Epigenetic Datasets

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Documentation for package ‘EpiCompare’ version 1.0.0

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

Help Pages

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
encode_H3K27ac	Example ChIP-seq peak file
EpiCompare	Compare epigenetic datasets
fragment_info	Summary on fragments
gather_files	Gather files
hg19_blacklist	Human genome hg19 blacklisted regions
hg38_blacklist	Human genome hg38 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_enrichment	Generate enrichment analysis plots
tidy_peakfile	Tidy peakfiles in GRanges
tss_plot	Read count frequency around TSS
width_boxplot	Peak width boxplot
write_example_peaks	Write example peaks