COHCAP

DOI: 10.18129/B9.bioc.COHCAP    

This is the development version of COHCAP; to use it, please install the devel version of Bioconductor.

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

Bioconductor version: Development (3.10)

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 "3.6") and enter:

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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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 1.31.0
In Bioconductor since BioC 2.14 (R-3.1) (5 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
Links To Me
Build Report  

Package Archives

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

Source Package COHCAP_1.31.0.tar.gz
Windows Binary COHCAP_1.31.0.zip
Mac OS X 10.11 (El Capitan) COHCAP_1.31.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/COHCAP
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/COHCAP
Package Short Url http://bioconductor.org/packages/COHCAP/
Package Downloads Report Download Stats

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