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:

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

To cite this package in a publication, start R and enter:

    citation("Rcade")

Documentation

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 Downloads

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)
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