To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("Rcade")

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

Rcade

 

   

This is the development version of Rcade; for the stable release version, see 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: Development (3.4)

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>

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

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://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

Details

biocViews ChIPSeq, DifferentialExpression, GeneExpression, Genetics, Sequencing, Software, Transcription
Version 1.15.1
In Bioconductor since BioC 2.11 (R-2.15) (4 years)
License GPL-2
Depends R (>= 2.14.0), methods, GenomicRanges, Rsamtools, baySeq
Imports utils, grDevices, stats, graphics, rgl, plotrix, S4Vectors, IRanges, GenomeInfoDb, GenomicAlignments
LinkingTo
Suggests limma, biomaRt, RUnit, BiocGenerics, BiocStyle
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 Rcade_1.15.1.tar.gz
Windows Binary Rcade_1.15.1.zip
Mac OS X 10.9 (Mavericks) Rcade_1.15.1.tgz
Subversion source (username/password: readonly)
Git source https://github.com/Bioconductor-mirror/Rcade
Package Short Url http://bioconductor.org/packages/Rcade/
Package Downloads Report Download Stats

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