# Assessment of duplication rates in RNA-Seq datasets

## Documentation for package ‘dupRadar’ version 1.12.1

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

## Help Pages

dupRadar-package | dupRadar.
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