EpiCompare is used to compare and analyse epigenetic datasets for quality control and benchmarking purposes. The package outputs an HTML report consisting of three sections: (1. General metrics) Metrics on peaks (percentage of blacklisted and non-standard peaks, and peak widths) and fragments (duplication rate) of samples, (2. Peak overlap) Percentage and statistical significance of overlapping and non-overlapping peaks. Also includes upset plot and (3. Functional annotation) functional annotation (ChromHMM, ChIPseeker and enrichment analysis) of peaks. Also includes peak enrichment around TSS.
Package details |
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Bioconductor views | ATACSeq ChIPSeq DNaseSeq Epigenetics FunctionalGenomics Genetics MultipleComparison QualityControl |
Maintainer | |
License | GPL-3 |
Version | 1.7.5 |
URL | https://github.com/neurogenomics/EpiCompare |
Package repository | View on GitHub |
Installation |
Install the latest version of this package by entering the following in R:
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