DOI: 10.18129/B9.bioc.Rcade    

This package is for version 3.15 of Bioconductor; for the 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: 3.15

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")):


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PDF R Script Rcade Vignette
PDF   Reference Manual
Text   NEWS


biocViews ChIPSeq, DifferentialExpression, GeneExpression, Genetics, Sequencing, Software, Transcription
Version 1.37.0
In Bioconductor since BioC 2.11 (R-2.15) (10 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
Suggests limma, biomaRt, RUnit, BiocGenerics, BiocStyle
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Source Package Rcade_1.37.0.tar.gz
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Source Repository git clone https://git.bioconductor.org/packages/Rcade
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Package Short Url https://bioconductor.org/packages/Rcade/
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