source("http://bioconductor.org/biocLite.R")
biocLite("CexoR")

CexoR

An R package to uncover high-resolution protein-DNA interactions in ChIP-exo replicates

Bioconductor version: 2.13

Strand specific peak-pair calling in ChIP-exo replicates. The cumulative Skellam distribution function (package 'skellam') is used to detect significant normalized count differences of opposed sign at each DNA strand (peak-pairs). Irreproducible discovery rate for overlapping peak-pairs across biological replicates is estimated using the package 'idr'.

Author: Pedro Madrigal <pm at engineering.com>

Maintainer: Pedro Madrigal <pm at engineering.com>

Installation

To install this package, start R and enter:

source("http://bioconductor.org/biocLite.R")
biocLite("CexoR")

Documentation

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

browseVignettes("CexoR")

 

PDF	R Script	CexoR Vignette
PDF		Reference Manual
Text		LICENSE

Details

biocViews	Genetics, Software, Transcription
Version	1.0.0
In Bioconductor since	BioC 2.13 (R-3.0)
License	Artistic-2.0 | GPL-2 + file LICENSE
Depends	R (>= 2.10.0), IRanges
Imports	Rsamtools, GenomicRanges, rtracklayer, idr
Suggests	RUnit, BiocGenerics
System Requirements
URL
Depends On Me
Imports Me
Suggests Me

Package Archives

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

Package Source	CexoR_1.0.0.tar.gz
Windows Binary	CexoR_1.0.0.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard)	CexoR_1.0.0.tgz
Browse/checkout source	(username/password: readonly)
Package Downloads Report	Download Stats