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EpiCompare
This is the released version of EpiCompare; for the devel version, see EpiCompare.
Comparison, Benchmarking & QC of Epigenomic Datasets
Bioconductor version: Release (3.22)
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.
Author: Sera Choi [aut] ORCID iD ORCID: 0000-0002-5077-1984 , Brian Schilder [aut] ORCID iD ORCID: 0000-0001-5949-2191 , Leyla Abbasova [aut], Alan Murphy [aut] ORCID iD ORCID: 0000-0002-2487-8753 , Nathan Skene [aut] ORCID iD ORCID: 0000-0002-6807-3180 , Thomas Roberts [ctb], Hiranyamaya Dash [cre] ORCID iD ORCID: 0009-0005-5514-505X
Maintainer: Hiranyamaya Dash <hdash.work at gmail.com>
citation("EpiCompare")):
Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("EpiCompare")
For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("EpiCompare")
Details
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Package Archives
Follow Installation instructions to use this package in your R session.