Learn R Programming

dupRadar (version 1.2.2)

Assessment of duplication rates in RNA-Seq datasets

Description

Duplication rate quality control for RNA-Seq datasets.

Copy Link

Version

Version

1.2.2

License

GPL-3

Maintainer

Sergi Sayols

Last Published

February 15th, 2017

Functions in dupRadar (1.2.2)

Duplication matrix of a failed RNASeq experiment

Duplication rate ~ total read count plot

Helper function used in getBinDuplication and getBinRpkMean

Report duplication stats on regions

Duplication rate ~ total read count fit model

readcountExpBoxplot

Barplot of percentage of reads falling into expression bins

cumulativeDuprateBarplot

Barplot showing the cumulative read counts fraction

getRpkCumulativeReadCountFraction

Helper function used in readcountExpressionBoxplot

getRpkBinReadCountFraction

Helper function used in readcountExpressionBoxplot

picardMarkDuplicates

Mark duplicates using Picard tools

bamutilMarkDuplicates

Mark duplicates using bamutil

dupRadar_examples

Example data containing precomputed matrices for two RNASeq experiments

getBinDuplication

Helper function used in duprateExpBoxplot

Duplication matrix of a good RNASeq experiment

Helper function used in duprateExpBoxplot

analyzeDuprates

Read in a BAM file and count the tags falling on the features described in the GTF file

getDynamicRange

duprateExpBoxplot

Duplication rate ~ total reads per kilobase (RPK) boxplot

Program dispatchers to mark duplicated reads from a BAM file

Draw histogram with the expression values

duprateExpDensPlot

Duplication rate ~ total read count plot

duprateExpIdentify

Identify genes plotted by duprateExpPlot