Introduction | Getting Started | Preparing Data | Visualizing Benchmarks | Specificity on expressed features. | Specificity on non-expressed features | Features expressed in one technical replicate but not the other. | Features expressed in neither replicates. | Specificity for genes only have two annotated transcripts | Sensitivity in differential analysis | ROC curves | Distribution of estimated fold changes | Summary | References
Package: rnaseqcomp 1.43.0
Mingxiang Teng
rnaseqcomp: Benchmarks for RNA-seq Quantification Pipelines
Several quantitative and visualized benchmarks for RNA-seq quantification pipelines. Two-condition quantifications for genes, transcripts, junctions or exons by each pipeline with necessary meta information should be organized into numeric matrices in order to proceed the evaluation.
Authors:
rnaseqcomp_1.43.0.tar.gz
rnaseqcomp_1.43.0.zip(r-4.7)rnaseqcomp_1.43.0.zip(r-4.6)rnaseqcomp_1.43.0.zip(r-4.5)
rnaseqcomp_1.43.0.tgz(r-4.6-any)rnaseqcomp_1.43.0.tgz(r-4.5-any)
rnaseqcomp_1.43.0.tar.gz(r-4.7-any)rnaseqcomp_1.43.0.tar.gz(r-4.6-any)
rnaseqcomp_1.43.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
rnaseqcomp/json (API)
| # Install 'rnaseqcomp' in R: |
| install.packages('rnaseqcomp', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/tengmx/rnaseqcomp/issues
Datasets:
- simdata - Example of Quantifications on Simulation Data
On BioConductor:rnaseqcomp-1.43.0(bioc 3.24)rnaseqcomp-1.42.0(bioc 3.23)
rnaseqvisualizationqualitycontrol
Last updated from:9c9e8539ed. Checks:1 ERROR, 7 NOTE, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | ERROR | 192 | ||
| linux-devel-x86_64 | NOTE | 185 | ||
| source / vignettes | OK | 176 | ||
| linux-release-x86_64 | NOTE | 158 | ||
| macos-release-arm64 | NOTE | 76 | ||
| macos-oldrel-arm64 | NOTE | 75 | ||
| windows-devel | NOTE | 84 | ||
| windows-release | NOTE | 74 | ||
| windows-oldrel | NOTE | 70 | ||
| wasm-release | OK | 97 |
Exports:plot2TXplotFCplotNEplotROCplotSDsignalCalibrate
Dependencies:RColorBrewer
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Sanity Check of S4 rnaseqcomp Class | check_rnaseqcomp |
| Estimate And Plot Transcript Proportion Difference | plot2TX |
| Estimate And Plot Fold Change Accuracy | plotFC |
| Estimate And Plot Express And Non-express Features | plotNE |
| Estimate And Plot Differential Expression | plotROC |
| Estimate And Plot Median Standard Deviation | plotSD |
| rnaseqcomp | rnaseqcomp-class |
| Quantification Filtering And Calibration | signalCalibrate |
| Example of Quantifications on Simulation Data | simdata |
