Assessment of duplication rates in RNA-Seq datasets

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Documentation for package ‘dupRadar’ version 1.36.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

analyzeDuprates	Read in a BAM file and count the tags falling on the features described in the GTF file
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 experiments
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 'getBinRpkMean'
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