dupRadar: Assessment of duplication rates in RNA-Seq datasets
Version 1.6.0

Duplication rate quality control for RNA-Seq datasets.

Browse man pages Browse package API and functions Browse package files

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
Version1.6.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("dupRadar")

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

Functions

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

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/CITATION
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
dupRadar documentation built on May 20, 2017, 9:55 p.m.