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 3.3 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: 3.3
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")
| R Script | COHCAP Vignette | |
| Reference Manual |
Details
| biocViews | DNAMethylation, DifferentialMethylation, Epigenetics, MethylSeq, Microarray, Software |
| Version | 1.10.0 |
| In Bioconductor since | BioC 2.14 (R-3.1) (2.5 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_1.10.0.tar.gz |
| Windows Binary | COHCAP_1.10.0.zip |
| Mac OS X 10.9 (Mavericks) | COHCAP_1.10.0.tgz |
| Subversion source | (username/password: readonly) |
| Git source | https://github.com/Bioconductor-mirror/COHCAP/tree/release-3.3 |
| Package Short Url | http://bioconductor.org/packages/COHCAP/ |
| Package Downloads Report | Download Stats |
Documentation »
Bioconductor
- Package vignettes and manuals.
- Workflows for learning and use.
- Course and conference material.
- Videos.
- Community resources and tutorials.
R / CRAN packages and documentation
Support »
Please read the posting guide. Post questions about Bioconductor to one of the following locations:
- Support site - for questions about Bioconductor packages
- Bioc-devel mailing list - for package developers
