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This is the development version of EpiCompare; for the stable release version, see EpiCompare.
Bioconductor version: Development (3.19)
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] , Brian Schilder [aut]
, Leyla Abbasova [aut], Alan Murphy [aut]
, Nathan Skene [aut]
, Thomas Roberts [cre]
Maintainer: Thomas Roberts <tomroberts.work15 at gmail.com>
Citation (from within R,
enter citation("EpiCompare")
):
To install this package, start R (version "4.4") 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.
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("EpiCompare")
HTML | R Script | docker |
HTML | R Script | EpiCompare |
HTML | R Script | example_report |
Reference Manual | ||
Text | NEWS |
Follow Installation instructions to use this package in your R session.
Source Package | EpiCompare_1.7.1.tar.gz |
Windows Binary | |
macOS Binary (x86_64) | EpiCompare_1.7.1.tgz |
macOS Binary (arm64) | |
Source Repository | git clone https://git.bioconductor.org/packages/EpiCompare |
Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/EpiCompare |
Bioc Package Browser | https://code.bioconductor.org/browse/EpiCompare/ |
Package Short Url | https://bioconductor.org/packages/EpiCompare/ |
Package Downloads Report | Download Stats |
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