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COHCAP

CpG Island Analysis Pipeline for Illumina Methylation Array and Targeted BS-Seq Data


Bioconductor version: Release (3.18)

COHCAP (pronounced "co-cap") provides a pipeline to analyze single-nucleotide resolution methylation data (Illumina 450k/EPIC methylation array, targeted BS-Seq, etc.). It provides differential methylation for CpG Sites, differential methylation for CpG Islands, integration with gene expression data, with visualizaton options. Discussion Group: https://sourceforge.net/p/cohcap/discussion/bioconductor/

Author: Charles Warden <cwarden at coh.org>, Yate-Ching Yuan <yyuan at coh.org>, Xiwei Wu <xwu at coh.org>

Maintainer: Charles Warden <cwarden at coh.org>

Citation (from within R, enter citation("COHCAP")):

Installation

To install this package, start R (version "4.3") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("COHCAP")

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("COHCAP")
COHCAP Vignette PDF R Script
Reference Manual PDF

Details

biocViews DNAMethylation, DifferentialMethylation, Epigenetics, MethylSeq, Microarray, Software
Version 1.48.0
In Bioconductor since BioC 2.14 (R-3.1) (10 years)
License GPL-3
Depends WriteXLS, COHCAPanno, RColorBrewer, gplots
Imports Rcpp, RcppArmadillo, BH
System Requirements Perl
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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package COHCAP_1.48.0.tar.gz
Windows Binary COHCAP_1.48.0.zip
macOS Binary (x86_64) COHCAP_1.48.0.tgz
macOS Binary (arm64) COHCAP_1.48.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/COHCAP
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/COHCAP
Bioc Package Browser https://code.bioconductor.org/browse/COHCAP/
Package Short Url https://bioconductor.org/packages/COHCAP/
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