To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("COHCAP")

In most cases, you don't need to download the package archive at all.

COHCAP

   

This package is for version 3.2 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: 3.2

This package provides a pipeline to analyze single-nucleotide resolution methylation data (Illumina 450k methylation array, targeted BS-Seq, etc.). It provides QC metrics, differential methylation for CpG Sites, differential methylation for CpG Islands, integration with gene expression data, and visualization of methylation values.

Author: Charles Warden

Maintainer: Charles Warden <cwarden45 at gmail.com>

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

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("COHCAP")

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("COHCAP")

 

PDF COHCAP Vignette
PDF   Reference Manual

Details

biocViews DNAMethylation, DifferentialMethylation, Epigenetics, MethylSeq, Microarray, Software
Version 1.8.0
In Bioconductor since BioC 2.14 (R-3.1) (2 years)
License GPL-3
Depends WriteXLS, COHCAPanno
Imports
LinkingTo
Suggests
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Build Report  

Package Archives

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

Package Source COHCAP_1.8.0.tar.gz
Windows Binary COHCAP_1.8.0.zip
Mac OS X 10.6 (Snow Leopard) COHCAP_1.8.0.tgz
Mac OS X 10.9 (Mavericks) COHCAP_1.8.0.tgz
Subversion source (username/password: readonly)
Git source https://github.com/Bioconductor-mirror/COHCAP/tree/release-3.2
Package Short Url http://bioconductor.org/packages/COHCAP/
Package Downloads Report Download Stats

Documentation »

Bioconductor

R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations:

Fred Hutchinson Cancer Research Center