Comparison, Benchmarking & QC of Epigenomic Datasets

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Documentation for package ‘EpiCompare’ version 1.4.0

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

Help Pages

bpplapply	Wrapper for bplapply
check_workers	Check workers
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
download_button	Download local file
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
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