dupRadar: Assessment of duplication rates in RNA-Seq datasets

Duplication rate quality control for RNA-Seq datasets.

Author
Sergi Sayols <sergisayolspuig@gmail.com>, Holger Klein <holger.klein@gmail.com>
Date of publication
None
Maintainer
Sergi Sayols <sergisayolspuig@gmail.com>, Holger Klein <holger.klein@gmail.com>
License
GPL-3
Version
1.4.0

View on Bioconductor

Man pages

analyzeDuprates
Read in a BAM file and count the tags falling on the features...
bamutilMarkDuplicates
Mark duplicates using bamutil
cumulativeDuprateBarplot
Barplot showing the cumulative read counts fraction
dm
Duplication matrix of a good RNASeq experiment
dm.bad
Duplication matrix of a failed RNASeq experiment
dupRadar
dupRadar.
dupRadar_examples
Example data containing precomputed matrices for two RNASeq...
duprateExpBoxplot
Duplication rate ~ total reads per kilobase (RPK) boxplot
duprateExpDensPlot
Duplication rate ~ total read count plot
duprateExpFit
Duplication rate ~ total read count fit model
duprateExpIdentify
Identify genes plotted by 'duprateExpPlot'
duprateExpPlot
Duplication rate ~ total read count plot
expressionHist
Draw histogram with the expression values
getBinDuplication
Helper function used in 'duprateExpBoxplot'
getBinRpkMean
Helper function used in 'duprateExpBoxplot'
getDupMatBin
Helper function used in 'getBinDuplication' and...
getDupMatStats
Report duplication stats on regions
getDynamicRange
Dynamic range
getRpkBinReadCountFraction
Helper function used in 'readcountExpressionBoxplot'
getRpkCumulativeReadCountFraction
Helper function used in 'readcountExpressionBoxplot'
markDuplicates
Program dispatchers to mark duplicated reads from a BAM file
picardMarkDuplicates
Mark duplicates using Picard tools
readcountExpBoxplot
Barplot of percentage of reads falling into expression bins

Files in this package

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