To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("COHCAP")
In most cases, you don't need to download the package archive at all.
COHCAP
CpG Island Analysis Pipeline for Illumina Methylation Array and Targeted BS-Seq Data
Bioconductor version: 3.0
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:
source("http://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 | 1.4.0 |
| In Bioconductor since | BioC 2.14 (R-3.1) |
| 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_1.4.0.tar.gz |
| Windows Binary | COHCAP_1.4.0.zip |
| Mac OS X 10.6 (Snow Leopard) | COHCAP_1.4.0.tgz |
| Mac OS X 10.9 (Mavericks) | COHCAP_1.4.0.tgz |
| Browse/checkout source | (username/password: readonly) |
| Package Downloads Report | Download Stats |
Common Bioconductor workflows include:
- Oligonucleotide Arrays
- High-throughput Sequencing
- Counting Reads for Differential Expression (parathyroideSE vignette)
- Annotation
- Annotating Variants
- Annotating Ranges
- Flow Cytometry and other assays
- Candidate Binding Sites for Known Transcription Factors
- Cloud-enabled cis-eQTL search and annotation
- RNA-Seq workflow: gene-level exploratory analysis and differential expression
- Changing genomic coordinate systems with rtracklayer::liftOver
- Mass spectrometry and proteomics data analysis
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