COHCAP

DOI: 10.18129/B9.bioc.COHCAP  

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

Bioconductor version: Release (3.16)

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>

Installation

To install this package, start R (version "4.2") 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")

 

PDF	R Script	COHCAP Vignette
PDF		Reference Manual

Details

biocViews	DNAMethylation, DifferentialMethylation, Epigenetics, MethylSeq, Microarray, Software
Version	1.44.0
In Bioconductor since	BioC 2.14 (R-3.1) (9 years)
License	GPL-3
Depends	WriteXLS, COHCAPanno, RColorBrewer, gplots
Imports	Rcpp, RcppArmadillo, BH
LinkingTo	Rcpp, BH
Suggests
SystemRequirements	Perl
Enhances
URL
Depends On Me
Imports Me
Suggests Me
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Build Report

Package Archives

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

Source Package	COHCAP_1.44.0.tar.gz
Windows Binary	COHCAP_1.44.0.zip (64-bit only)
macOS Binary (x86_64)	COHCAP_1.44.0.tgz
macOS Binary (arm64)	COHCAP_1.44.0.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/
Package Downloads Report	Download Stats