COHCAP
This package is for version 3.19 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see .
CpG Island Analysis Pipeline for Illumina Methylation Array and Targeted BS-Seq Data
Bioconductor version: Development (3.19)
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("COHCAP")):
Installation
To install this package, start R (version "4.4") 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 | R Script | |
| Reference Manual |
Details
| biocViews | DNAMethylation, DifferentialMethylation, Epigenetics, MethylSeq, Microarray, Software |
| Version | 1.49.0 |
| In Bioconductor since | BioC 2.14 (R-3.1) (10 years) |
| License | GPL-3 |
| Depends | WriteXLS, COHCAPanno, RColorBrewer, gplots |
| Imports | Rcpp, RcppArmadillo, BH |
| System Requirements | Perl |
| URL |
See More
| Suggests | |
| Linking To | Rcpp, BH |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | COHCAP_1.49.0.tar.gz |
| Windows Binary | COHCAP_1.49.0.zip |
| macOS Binary (x86_64) | COHCAP_1.49.0.tgz |
| macOS Binary (arm64) | COHCAP_1.49.0.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 |