Package: PROPER 1.44.0
Hao Wu
PROPER: PROspective Power Evaluation for RNAseq
This package provide simulation based methods for evaluating the statistical power in differential expression analysis from RNA-seq data.
Authors:
PROPER_1.44.0.tar.gz
PROPER_1.44.0.zip(r-4.7)PROPER_1.44.0.zip(r-4.6)PROPER_1.44.0.zip(r-4.5)
PROPER_1.44.0.tgz(r-4.6-any)PROPER_1.44.0.tgz(r-4.5-any)
PROPER_1.44.0.tar.gz(r-4.7-any)PROPER_1.44.0.tar.gz(r-4.6-any)
PROPER_1.44.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
PROPER/json (API)
| # Install 'PROPER' in R: |
| install.packages('PROPER', repos = c('https://bioc-release.r-universe.dev', 'https://cloud.r-project.org')) |
- GE.human - Some existing RNA-seq and gene expression microarray data
- param - Some existing RNA-seq and gene expression microarray data
- param - Some existing RNA-seq and gene expression microarray data
- param - Some existing RNA-seq and gene expression microarray data
- param - Some existing RNA-seq and gene expression microarray data
- pbmc - Some existing RNA-seq and gene expression microarray data
On BioConductor:PROPER-1.45.0(bioc 3.24)PROPER-1.44.0(bioc 3.23)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
immunooncologysequencingrnaseqdifferentialexpression
Last updated from:1d8c9e7b6f (on RELEASE_3_23). Checks:1 ERROR, 7 WARNING, 2 OK. Indexed: no.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | ERROR | 160 | ||
| linux-devel-x86_64 | WARNING | 186 | ||
| source / vignettes | OK | 324 | ||
| linux-release-x86_64 | WARNING | 217 | ||
| macos-release-arm64 | WARNING | 88 | ||
| macos-oldrel-arm64 | WARNING | 124 | ||
| windows-devel | WARNING | 172 | ||
| windows-release | WARNING | 112 | ||
| windows-oldrel | WARNING | 115 | ||
| wasm-release | OK | 140 |
Exports:comparePowerestParamplotAllplotFDcostplotFDRplotPowerplotPowerAlphaplotPowerFDplotPowerHistplotPowerTDpower.seqDepthRNAseq.SimOptions.2grprunSimssimRNAseqsummaryPower
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Compute the power-related quantities from simulation results | comparePower |
| estimate simulation parameters from a count table | estParam |
| Some existing RNA-seq and gene expression microarray data | bottomly cheung GE.human gilad maqc param pbmc |
| Plot the histogram of power | plotPowerHist |
| Plot the stratified curves for power-related quantities | plotAll plotFDcost plotFDR plotPower plotPowerAlpha plotPowerFD plotPowerTD |
| Estimate the marginal power under different sequencing depth | power.seqDepth |
| Set up options for simulating RNA-seq data in two-group comparison. | RNAseq.SimOptions.2grp |
| Run a number of RNA-seq simulations and DE detections | runSims |
| Simulate RNA-seq count data | simRNAseq |
| Generate a summary table for power analysis result | summaryPower |
