This site is a development preview. As such the content and styling may not be final and is subject to change before going into production. To see more information about the redesign click here.

Menu

Documentation:

R / CRAN packages and documentation

Support

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

COHCAP

This is the development version of COHCAP; for the stable release version, see COHCAP.

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

Bioconductor version: Development (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")

# 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")
COHCAP Vignette PDF R Script
Reference Manual PDF

Details

biocViews DNAMethylation, DifferentialMethylation, Epigenetics, MethylSeq, Microarray, Software
Version 1.47.0
In Bioconductor since BioC 2.14 (R-3.1) (9.5 years)
License GPL-3
Depends WriteXLS, COHCAPanno, RColorBrewer, gplots
Imports Rcpp, RcppArmadillo, BH
Linking To Rcpp, BH
Suggests
System Requirements Perl
Enhances
URL
See More
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_1.47.0.tar.gz
Windows Binary COHCAP_1.47.0.zip (64-bit only)
macOS Binary (x86_64) COHCAP_1.47.0.tgz
macOS Binary (arm64) COHCAP_1.47.0.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