dupRadar: Assessment of duplication rates in RNA-Seq datasets

Duplication rate quality control for RNA-Seq datasets.

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("dupRadar")
AuthorSergi Sayols <sergisayolspuig@gmail.com>, Holger Klein <holger.klein@gmail.com>
Bioconductor views QualityControl RNASeq Sequencing Technology
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

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

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

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