Comparison, Benchmarking & QC of Epigenomic Datasets
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Documentation for package ‘EpiCompare’ version 1.2.0
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 |