Introduction to dupRadar | Getting started using dupRadar | Preparing your data | A GTF file | AnnotationHub as a source of GTF files | dupRate demo data | The duplication rate analysis | Plotting and interpretation | Fitting a model into the data | Comparing the fitted parameters to other datasets | Other plots | Other information deduced from the data | Fraction of multimappers per gene | Connection between possible PCR artefacts and GC content | Conclusion | Including dupRadar into pipelines | Citing dupRadar | Reporting problems or bugs | Session info
Package: dupRadar 1.43.0
Sergi Sayols
dupRadar: Assessment of duplication rates in RNA-Seq datasets
Duplication rate quality control for RNA-Seq datasets.
Authors:
dupRadar_1.43.0.tar.gz
dupRadar_1.43.0.zip(r-4.7-any)dupRadar_1.43.0.zip(r-4.6-any)dupRadar_1.43.0.zip(r-4.5-any)
dupRadar_1.43.0.tgz(r-4.6-any)dupRadar_1.43.0.tgz(r-4.5-any)
dupRadar_1.43.0.tar.gz(r-4.7-any)dupRadar_1.43.0.tar.gz(r-4.6-any)
dupRadar_1.43.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
dupRadar/json (API)
| # 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
Datasets:
- dupRadar_examples - Example data containing precomputed matrices for two RNASeq experiments
On BioConductor:dupRadar-1.43.0(bioc 3.24)dupRadar-1.42.0(bioc 3.23)
technologysequencingrnaseqqualitycontrolimmunooncology
Last updated from:26451be093. Checks:4 ERROR, 4 NOTE, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | ERROR | 135 | ||
| linux-devel | NOTE | 185 | ||
| source / vignettes | OK | 350 | ||
| linux-release | NOTE | 226 | ||
| macos-release | NOTE | 147 | ||
| macos-oldrel | NOTE | 134 | ||
| windows-devel | ERROR | 80 | ||
| windows-release | ERROR | 86 | ||
| windows-oldrel | ERROR | 86 | ||
| wasm-release | OK | 98 |
Exports:analyzeDupratescumulativeDuprateBarplotduprateExpBoxplotduprateExpDensPlotduprateExpFitduprateExpIdentifyduprateExpPlotexpressionHistgetBinDuplicationgetBinRpkMeangetDupMatBingetDupMatStatsgetDynamicRangegetRpkBinReadCountFractiongetRpkCumulativeReadCountFractionmarkDuplicatesreadcountExpBoxplot
Dependencies:KernSmoothlatticeMatrixRsubread
