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.

AuthorJonathan Cairns
Date of publicationNone
MaintainerJonathan Cairns <jmcairns200@gmail.com>
LicenseGPL-2
Version1.16.0

View on Bioconductor

Functions

constructRcadeTable Man page
countReads Man page
defineBins Man page
diffCountsBaySeq Man page
exportRcade Man page
exportRcade-methods Man page
exportRcade,Rcade-method Man page
getChIP Man page
getChIP<- Man page
getChIP<-,Rcade-method Man page
getChIP,Rcade-method Man page
getDE Man page
getDE<- Man page
getDE<-,Rcade-method Man page
getDE,Rcade-method Man page
getRcade Man page
getRcade<- Man page
getRcade<-,Rcade-method Man page
getRcade,Rcade-method Man page
plotBB Man page
plotBBB Man page
plotBBB,Rcade-method Man page
plotBB,Rcade-method Man page
plotMM Man page
plotMM,Rcade-method Man page
plotPCA Man page
plotPCA,Rcade-method Man page
RcadeAnalysis Man page
Rcade-class Man page
RcadeSTAT1 Man page
RcadeTrack-class Man page

Files

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

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.