Rcade

DOI: 10.18129/B9.bioc.Rcade  

This package is deprecated. It will probably be removed from Bioconductor. Please refer to the package end-of-life guidelines for more information.

This package is for version 3.16 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: Release (3.16)

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>

Installation

To install this package, start R (version "4.2") 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")

 

PDF	R Script	Rcade Vignette
PDF		Reference Manual
Text		README
Text		NEWS

Details

biocViews	ChIPSeq, DifferentialExpression, GeneExpression, Genetics, Sequencing, Software, Transcription
Version	1.39.1
In Bioconductor since	BioC 2.11 (R-2.15) (10.5 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
LinkingTo
Suggests	limma, biomaRt, RUnit, BiocGenerics, BiocStyle
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	Rcade_1.39.1.tar.gz
Windows Binary	Rcade_1.39.1.zip
macOS Binary (x86_64)
macOS Binary (arm64)	Rcade_1.40.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/Rcade
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/Rcade
Package Short Url	https://bioconductor.org/packages/Rcade/
Package Downloads Report	Download Stats