To install this package, start R and enter:

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

In most cases, you don't need to download the package archive at all.

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: Release (2.14)

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>

To install this package, start R and enter:

Citation (from within R, enter citation("Rcade")):

Installation

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 1.6.0
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, BiocStyle
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_1.6.0.tar.gz
Windows Binary Rcade_1.6.0.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard) Rcade_1.6.0.tgz
Mac OS X 10.9 (Mavericks) Rcade_1.6.0.tgz
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