Rcade

This package is for version 3.14 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: 3.14

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>

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

Installation

To install this package, start R (version "4.1") 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 1.36.0
In Bioconductor since BioC 2.11 (R-2.15) (11.5 years)
License GPL-2
Depends R (>= 3.5.0), methods, GenomicRanges, Rsamtools, baySeq
Imports utils, grDevices, stats, graphics, rgl, plotrix, S4Vectors(>= 0.23.19), IRanges, GenomeInfoDb, GenomicAlignments
System Requirements
URL
See More
Suggests limma, biomaRt, RUnit, BiocGenerics, BiocStyle
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report Build Report

Package Archives

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

Source Package Rcade_1.36.0.tar.gz
Windows Binary Rcade_1.36.0.zip
macOS 10.13 (High Sierra) Rcade_1.36.0.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 3.14 Source Archive