dupRadar: Assessment of duplication rates in RNA-Seq datasets

Duplication rate quality control for RNA-Seq datasets.

AuthorSergi Sayols <sergisayolspuig@gmail.com>, Holger Klein <holger.klein@gmail.com>
Date of publicationNone
MaintainerSergi Sayols <sergisayolspuig@gmail.com>, Holger Klein <holger.klein@gmail.com>
LicenseGPL-3
Version1.4.0

View on Bioconductor

Functions

analyzeDuprates Man page
bamutilMarkDuplicates Man page
cumulativeDuprateBarplot Man page
dm Man page
dm.bad Man page
dupRadar Man page
dupRadar_examples Man page
dupRadar-package Man page
duprateExpBoxplot Man page
duprateExpDensPlot Man page
duprateExpFit Man page
duprateExpIdentify Man page
duprateExpPlot Man page
expressionHist Man page
getBinDuplication Man page
getBinRpkMean Man page
getDupMatBin Man page
getDupMatStats Man page
getDynamicRange Man page
getRpkBinReadCountFraction Man page
getRpkCumulativeReadCountFraction Man page
markDuplicates Man page
picardMarkDuplicates Man page
readcountExpBoxplot Man page

Files

dupRadar/.BBSoptions
dupRadar/DESCRIPTION
dupRadar/NAMESPACE
dupRadar/NEWS
dupRadar/R
dupRadar/R/analyzeDuprates.R dupRadar/R/cumulativeDuprateBarplot.R dupRadar/R/dupRadar.R dupRadar/R/duprateExpBoxplot.R dupRadar/R/duprateExpDensPlot.R dupRadar/R/duprateExpFit.R dupRadar/R/duprateExpIdentify.R dupRadar/R/duprateExpPlot.R dupRadar/R/expressionHist.R dupRadar/R/getBinDuplication.R dupRadar/R/getBinRpkMean.R dupRadar/R/getDupMatBin.R dupRadar/R/getDupMatStats.R dupRadar/R/getDynamicRange.R dupRadar/R/getRpkBinReadCountFraction.R dupRadar/R/getRpkCumulativeReadCountFraction.R dupRadar/R/markDuplicates.R dupRadar/R/readcountExpBoxplot.R
dupRadar/build
dupRadar/build/vignette.rds
dupRadar/data
dupRadar/data/datalist
dupRadar/data/dupRadar_examples.RData
dupRadar/inst
dupRadar/inst/doc
dupRadar/inst/doc/dupRadar.R
dupRadar/inst/doc/dupRadar.Rmd
dupRadar/inst/doc/dupRadar.html
dupRadar/inst/extdata
dupRadar/inst/extdata/genes.gtf
dupRadar/inst/extdata/wgEncodeCaltechRnaSeqGm12878R1x75dAlignsRep2V2.bam
dupRadar/inst/extdata/wgEncodeCaltechRnaSeqGm12878R1x75dAlignsRep2V2.bam.bai
dupRadar/inst/extdata/wgEncodeCaltechRnaSeqGm12878R1x75dAlignsRep2V2_duprm.bam
dupRadar/inst/extdata/wgEncodeCaltechRnaSeqGm12878R1x75dAlignsRep2V2_duprm.bam.log
dupRadar/man
dupRadar/man/analyzeDuprates.Rd dupRadar/man/bamutilMarkDuplicates.Rd dupRadar/man/cumulativeDuprateBarplot.Rd dupRadar/man/dm.Rd dupRadar/man/dm.bad.Rd dupRadar/man/dupRadar.Rd dupRadar/man/dupRadar_examples.Rd dupRadar/man/duprateExpBoxplot.Rd dupRadar/man/duprateExpDensPlot.Rd dupRadar/man/duprateExpFit.Rd dupRadar/man/duprateExpIdentify.Rd dupRadar/man/duprateExpPlot.Rd dupRadar/man/expressionHist.Rd dupRadar/man/getBinDuplication.Rd dupRadar/man/getBinRpkMean.Rd dupRadar/man/getDupMatBin.Rd dupRadar/man/getDupMatStats.Rd dupRadar/man/getDynamicRange.Rd dupRadar/man/getRpkBinReadCountFraction.Rd dupRadar/man/getRpkCumulativeReadCountFraction.Rd dupRadar/man/markDuplicates.Rd dupRadar/man/picardMarkDuplicates.Rd dupRadar/man/readcountExpBoxplot.Rd
dupRadar/vignettes
dupRadar/vignettes/dupRadar.Rmd
dupRadar/vignettes/figures
dupRadar/vignettes/figures/GCcontent.svg
dupRadar/vignettes/figures/GCdependence.png
dupRadar/vignettes/figures/encode.svg

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

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