Package: dupRadar 1.37.0

Sergi Sayols

dupRadar: Assessment of duplication rates in RNA-Seq datasets

Duplication rate quality control for RNA-Seq datasets.

Authors:Sergi Sayols <sergisayolspuig@gmail.com>, Holger Klein <holger.klein@gmail.com>

dupRadar_1.37.0.tar.gz
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dupRadar.pdf |dupRadar.html
dupRadar/json (API)
NEWS

# Install 'dupRadar' in R:
install.packages('dupRadar', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/ssayols/dupradar/issues

Datasets:
  • dupRadar_examples - Example data containing precomputed matrices for two RNASeq experiments

On BioConductor:dupRadar-1.37.0(bioc 3.21)dupRadar-1.36.0(bioc 3.20)

technologysequencingrnaseqqualitycontrolimmunooncology

6.48 score 1 stars 60 scripts 310 downloads 23 mentions 17 exports 4 dependencies

Last updated 2 months agofrom:9afe62b26f. Checks:OK: 1 NOTE: 6. Indexed: yes.

TargetResultDate
Doc / VignettesOKDec 18 2024
R-4.5-winNOTEDec 18 2024
R-4.5-linuxNOTEDec 18 2024
R-4.4-winNOTEDec 18 2024
R-4.4-macNOTEDec 18 2024
R-4.3-winNOTEDec 18 2024
R-4.3-macNOTEDec 18 2024

Exports:analyzeDupratescumulativeDuprateBarplotduprateExpBoxplotduprateExpDensPlotduprateExpFitduprateExpIdentifyduprateExpPlotexpressionHistgetBinDuplicationgetBinRpkMeangetDupMatBingetDupMatStatsgetDynamicRangegetRpkBinReadCountFractiongetRpkCumulativeReadCountFractionmarkDuplicatesreadcountExpBoxplot

Dependencies:KernSmoothlatticeMatrixRsubread

Using the dupRadar package

Rendered fromdupRadar.Rmdusingknitr::rmarkdownon Dec 18 2024.

Last update: 2020-02-27
Started: 2015-09-28

Citation

Sergi Sayols, Denise Scherzinger and Holger Klein (2016): dupRadar: a Bioconductor package for the assessment of PCR artifacts in RNA-Seq data. BMC Bioinformatics, 17:428,<doi:10.1186/s12859-016-1276-2>

Corresponding BibTeX entry:

  @Article{,
    title = {dupRadar: a Bioconductor package for the assessment of PCR
      artifacts in RNA-Seq data},
    author = {Sergi Sayols and Denise Scherzinger and Holger Klein},
    year = {2016},
    journal = {BMC Bioinformatics},
    doi = {10.1186/s12859-016-1276-2},
    url = {http://dx.doi.org/10.1186/s12859-016-1276-2},
    volume = {17},
    issue = {1},
    pages = {428},
  }

Readme and manuals

dupRadar

Assessment of duplication rates in RNA-Seq datasets.

Introduction to dupRadar

PCR clonal artefacts originating from NGS library preparation can affect both genomic as well as RNA-Seq applications when protocols are pushed to their limits. In RNA-Seq however the artifactual reads are not easy to tell apart from normal read duplication due to natural over-sequencing of highly expressed genes. Especially when working with little input material or single cells assessing the fraction of duplicate reads is an important quality control step for NGS data sets. Up to now there are only tools to calculate the global duplication rates that do not take into account the effect of gene expression levels which leaves them of limited use for RNA-Seq data.

Installation

To install this package, start R and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("dupRadar")

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("dupRadar")

or access the pkgdown documentation.

Dependencies

Imports (mandatory for core functionality)
  • Rsubread: Mapping, quantification and variant analysis of sequencing data.

Citation

Sayols S, Scherzinger D, Klein H (2016). "dupRadar: a Bioconductor package for the assessment of PCR artifacts in RNA-Seq data." BMC Bioinformatics, 17, 428. doi: 10.1186/s12859-016-1276-2.

Help Manual

Help pageTopics
Read in a BAM file and count the tags falling on the features described in the GTF fileanalyzeDuprates
Mark duplicates using bamutilbamutilMarkDuplicates
Barplot showing the cumulative read counts fractioncumulativeDuprateBarplot
Duplication matrix of a good RNASeq experimentdm
Duplication matrix of a failed RNASeq experimentdm.bad
dupRadar.dupRadar
Example data containing precomputed matrices for two RNASeq experimentsdupRadar_examples
Duplication rate ~ total reads per kilobase (RPK) boxplotduprateExpBoxplot
Duplication rate ~ total read count plotduprateExpDensPlot
Duplication rate ~ total read count fit modelduprateExpFit
Identify genes plotted by 'duprateExpPlot'duprateExpIdentify
Duplication rate ~ total read count plotduprateExpPlot
Draw histogram with the expression valuesexpressionHist
Helper function used in 'duprateExpBoxplot'getBinDuplication
Helper function used in 'duprateExpBoxplot'getBinRpkMean
Helper function used in 'getBinDuplication' and 'getBinRpkMean'getDupMatBin
Report duplication stats on regionsgetDupMatStats
Dynamic rangegetDynamicRange
Helper function used in 'readcountExpressionBoxplot'getRpkBinReadCountFraction
Helper function used in 'readcountExpressionBoxplot'getRpkCumulativeReadCountFraction
Program dispatchers to mark duplicated reads from a BAM filemarkDuplicates
Mark duplicates using Picard toolspicardMarkDuplicates
Barplot of percentage of reads falling into expression binsreadcountExpBoxplot