Package: dupRadar 1.37.0
dupRadar: Assessment of duplication rates in RNA-Seq datasets
Duplication rate quality control for RNA-Seq datasets.
Authors:
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')) |
Bug tracker:https://github.com/ssayols/dupradar/issues
- 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
Last updated 2 months agofrom:9afe62b26f. Checks:OK: 1 NOTE: 6. Indexed: yes.
Target | Result | Date |
---|---|---|
Doc / Vignettes | OK | Dec 18 2024 |
R-4.5-win | NOTE | Dec 18 2024 |
R-4.5-linux | NOTE | Dec 18 2024 |
R-4.4-win | NOTE | Dec 18 2024 |
R-4.4-mac | NOTE | Dec 18 2024 |
R-4.3-win | NOTE | Dec 18 2024 |
R-4.3-mac | NOTE | Dec 18 2024 |
Exports:analyzeDupratescumulativeDuprateBarplotduprateExpBoxplotduprateExpDensPlotduprateExpFitduprateExpIdentifyduprateExpPlotexpressionHistgetBinDuplicationgetBinRpkMeangetDupMatBingetDupMatStatsgetDynamicRangegetRpkBinReadCountFractiongetRpkCumulativeReadCountFractionmarkDuplicatesreadcountExpBoxplot
Dependencies:KernSmoothlatticeMatrixRsubread
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.