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

Rcade

R-based analysis of ChIP-seq And Differential Expression - a tool for integrating a count-based ChIP-seq analysis with differential expression summary data.

Bioconductor version: 2.13

Rcade (which stands for "R-based analysis of ChIP-seq And Differential Expression") is a tool for integrating ChIP-seq data with differential expression summary data, through a Bayesian framework. A key application is in identifing the genes targeted by a transcription factor of interest - that is, we collect genes that are associated with a ChIP-seq peak, and differential expression under some perturbation related to that TF.

Author: Jonathan Cairns

Maintainer: Jonathan Cairns <jmcairns200 at gmail.com>

Installation

To install this package, start R and enter:

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

Documentation

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

browseVignettes("Rcade")

 

PDF	R Script	Rcade Vignette
PDF		Reference Manual
Text		README
Text		NEWS

Details

biocViews	ChIPseq, DifferentialExpression, GeneExpression, Genetics, Sequencing, Software, Transcription
Version	1.4.0
In Bioconductor since	BioC 2.11 (R-2.15)
License	GPL-2
Depends	R (>= 2.14.0), methods, GenomicRanges, baySeq, Rsamtools
Imports	graphics, IRanges, rgl
Suggests	limma, biomaRt, 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	Rcade_1.4.0.tar.gz
Windows Binary	Rcade_1.4.0.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard)	Rcade_1.4.0.tgz
Browse/checkout source	(username/password: readonly)
Package Downloads Report	Download Stats