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: 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>
citation("Rcade")):
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")| Rcade Vignette | R Script | |
| Reference Manual | ||
| README | Text | |
| NEWS | Text |
Details
| biocViews | ChIPSeq, DifferentialExpression, GeneExpression, Genetics, Sequencing, Software, Transcription |
| Version | 1.39.1 |
| 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_1.39.1.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 |
| Old Source Packages for BioC 3.16 | Source Archive |