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
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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 (3.4)
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")
| R Script | Rcade Vignette | |
| Reference Manual | ||
| Text | README | |
| Text | NEWS |
Details
| biocViews | ChIPSeq, DifferentialExpression, GeneExpression, Genetics, Sequencing, Software, Transcription |
| Version | 1.16.0 |
| In Bioconductor since | BioC 2.11 (R-2.15) (4.5 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 | |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | Rcade_1.16.0.tar.gz |
| Windows Binary | Rcade_1.16.0.zip |
| Mac OS X 10.9 (Mavericks) | Rcade_1.16.0.tgz |
| Subversion source | (username/password: readonly) |
| Git source | https://github.com/Bioconductor-mirror/Rcade/tree/release-3.4 |
| Package Short Url | http://bioconductor.org/packages/Rcade/ |
| Package Downloads Report | Download Stats |
Documentation »
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