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 (2.11)
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 <jonathan.cairns at cancer.org.uk>
To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("Rcade")
To cite this package in a publication, start R and enter:
citation("Rcade")
Documentation
| R Script | Rcade Vignette | |
| Reference Manual | ||
| Text | README | |
| Text | NEWS |
Details
| biocViews | ChIPseq, DifferentialExpression, GeneExpression, Genetics, Sequencing, Software, Transcription |
| Version | 1.0.0 |
| In Bioconductor since | BioC 2.11 (R-2.15) |
| License | GPL-2 |
| Depends | R (>= 2.14.0), methods, GenomicRanges, baySeq, Rsamtools |
| Imports | graphics, IRanges, rgl |
| Suggests | limma, biomaRt, RUnit, BiocGenerics |
| System Requirements | |
| URL | |
| Depends On Me | |
| Imports Me | |
| Suggests Me |
Package Downloads
| Package Source | Rcade_1.0.0.tar.gz |
| Windows Binary | Rcade_1.0.0.zip (32- & 64-bit) |
| MacOS 10.5 (Leopard) | Rcade_1.0.0.tgz |
| Package Downloads Report | Download Stats |
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