EpiCompare

This is the development version of EpiCompare; for the stable release version, see EpiCompare.

Comparison, Benchmarking & QC of Epigenomic Datasets

Platform availability badge Ranking badge Support activity badge Years in BioConductor badge Build results badge Last commit badge Dependency count badge

DOI: 10.18129/B9.bioc.EpiCompare

Bioconductor version: Development (3.23)

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 (from within R, enter citation("EpiCompare")):

Installation

To install this package, start R (version "4.6") and enter:


if (!require("BiocManager", quietly = TRUE))
 install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
BiocManager::install("EpiCompare")

For older versions of R, please refer to the appropriate Bioconductor release.