Rcade

This package is for version 3.9 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date 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: 3.9

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 (version "3.6") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("Rcade")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

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

browseVignettes("Rcade")
Rcade Vignette PDF R Script
Reference Manual PDF
README Text
NEWS Text

Details

biocViews ChIPSeq, DifferentialExpression, GeneExpression, Genetics, Sequencing, Software, Transcription
Version 1.26.0
In Bioconductor since BioC 2.11 (R-2.15) (11.5 years)
License GPL-2
Depends R (>= 2.14.0), methods, GenomicRanges, Rsamtools, baySeq
Imports utils, grDevices, stats, graphics, rgl, plotrix, S4Vectors, IRanges, GenomeInfoDb, GenomicAlignments
System Requirements
URL
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Suggests limma, biomaRt, RUnit, BiocGenerics, BiocStyle
Linking To
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Depends On Me
Imports Me
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Build Report Build Report

Package Archives

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

Source Package Rcade_1.26.0.tar.gz
Windows Binary Rcade_1.26.0.zip (64-bit only)
Mac OS X 10.11 (El Capitan) Rcade_1.26.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/Rcade
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/Rcade
Bioc Package Browser https://code.bioconductor.org/browse/Rcade/
Package Short Url https://bioconductor.org/packages/Rcade/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.9 Source Archive