COHCAP

DOI: 10.18129/B9.bioc.COHCAP    

This package is for version 3.8 of Bioconductor; for the stable, up-to-date release version, see COHCAP.

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

Bioconductor version: 3.8

This package 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 <cwarden45 at gmail.com>

Installation

To install this package, start R (version "3.5") and enter:

if (!requireNamespace("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	1.28.1
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_1.28.1.tar.gz
Windows Binary	COHCAP_1.28.1.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan)	COHCAP_1.28.1.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