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

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
Date of publication
None
Maintainer
Jonathan Cairns <jmcairns200@gmail.com>
License
GPL-2
Version
1.16.0

View on Bioconductor

Man pages

constructRcadeTable
Construct Rcade Table
countReads
Count Reads
defineBins
Define Bins
diffCountsBaySeq
Differential Counts wrapper - BaySeq
exportRcade-methods
exportRcade and ...
RcadeAnalysis
Rcade Analysis
Rcade-class
Rcade Class
RcadeSTAT1
Rcade object - STAT1 data
RcadeTrack-class
RcadeTrack Class

Files in this package

Rcade/.BBSoptions
Rcade/DESCRIPTION
Rcade/NAMESPACE
Rcade/NEWS
Rcade/R
Rcade/R/AllClasses.R
Rcade/R/AllGenerics.R
Rcade/R/Rcade-Methods.R
Rcade/R/Rcade-OutputMethods.R
Rcade/R/Rcade-PlotMethods.R
Rcade/R/RcadeAnalysis.R
Rcade/R/RcadeTrack-Methods.R
Rcade/R/aaa.R
Rcade/R/checkTargets.R
Rcade/R/constructRcadeTable.R
Rcade/R/countReads.R
Rcade/R/defineBins.R
Rcade/R/diffCountsBaySeq.R
Rcade/R/sanitizeDElookup.R
Rcade/R/zzz.R
Rcade/README
Rcade/TODO
Rcade/build
Rcade/build/vignette.rds
Rcade/data
Rcade/data/RcadeSTAT1.rda
Rcade/data/datalist
Rcade/inst
Rcade/inst/CITATION
Rcade/inst/doc
Rcade/inst/doc/Rcade.R
Rcade/inst/doc/Rcade.Rnw
Rcade/inst/doc/Rcade.pdf
Rcade/inst/extdata
Rcade/inst/extdata/STAT1
Rcade/inst/extdata/STAT1/DE.csv
Rcade/inst/extdata/STAT1/anno.csv
Rcade/inst/extdata/STAT1/targets.csv
Rcade/inst/extdata/STAT1/wgEncodeSydhTfbsHelas3InputIfng30StdAlnRep1.bam
Rcade/inst/extdata/STAT1/wgEncodeSydhTfbsHelas3InputIfng30StdAlnRep1.bam.bai
Rcade/inst/extdata/STAT1/wgEncodeSydhTfbsHelas3InputStdAlnRep1.bam
Rcade/inst/extdata/STAT1/wgEncodeSydhTfbsHelas3InputStdAlnRep1.bam.bai
Rcade/inst/extdata/STAT1/wgEncodeSydhTfbsHelas3Stat1Ifng30StdAlnRep1.bam
Rcade/inst/extdata/STAT1/wgEncodeSydhTfbsHelas3Stat1Ifng30StdAlnRep1.bam.bai
Rcade/inst/extdata/STAT1/wgEncodeSydhTfbsHelas3Stat1Ifng30StdAlnRep2.bam
Rcade/inst/extdata/STAT1/wgEncodeSydhTfbsHelas3Stat1Ifng30StdAlnRep2.bam.bai
Rcade/inst/unitTests
Rcade/inst/unitTests/test_modules.R
Rcade/man
Rcade/man/Rcade-class.Rd
Rcade/man/RcadeAnalysis.Rd
Rcade/man/RcadeSTAT1.Rd
Rcade/man/RcadeTrack-class.Rd
Rcade/man/constructRcadeTable.Rd
Rcade/man/countReads.Rd
Rcade/man/defineBins.Rd
Rcade/man/diffCountsBaySeq.Rd
Rcade/man/exportRcade-methods.Rd
Rcade/tests
Rcade/tests/runTests.R
Rcade/vignettes
Rcade/vignettes/Rcade.Rnw
Rcade/vignettes/plotBBB.png