This package is for version 3.8 of Bioconductor; for the stable, up-to-date release version, see Rcade.
Bioconductor version: 3.8
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")
):
To install this package, start R (version "3.5") and enter:
if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("Rcade")
For older versions of R, please refer to the appropriate Bioconductor release.
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("Rcade")
R Script | Rcade Vignette | |
Reference Manual | ||
Text | README | |
Text | NEWS |
biocViews | ChIPSeq, DifferentialExpression, GeneExpression, Genetics, Sequencing, Software, Transcription |
Version | 1.24.0 |
In Bioconductor since | BioC 2.11 (R-2.15) (6.5 years) |
License | GPL-2 |
Depends | R (>= 2.14.0), methods, GenomicRanges, Rsamtools, baySeq |
Imports | utils, grDevices, stats, graphics, rgl, plotrix, S4Vectors, IRanges, GenomeInfoDb, GenomicAlignments |
LinkingTo | |
Suggests | limma, biomaRt, RUnit, BiocGenerics, BiocStyle |
SystemRequirements | |
Enhances | |
URL | |
Depends On Me | |
Imports Me | |
Suggests Me | |
Links To Me | |
Build Report |
Follow Installation instructions to use this package in your R session.
Source Package | Rcade_1.24.0.tar.gz |
Windows Binary | Rcade_1.24.0.zip |
Mac OS X 10.11 (El Capitan) | Rcade_1.24.0.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 | http://bioconductor.org/packages/Rcade/ |
Package Downloads Report | Download Stats |
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