Package: PROPER 1.39.0
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_1.39.0.tar.gz
PROPER_1.39.0.zip(r-4.5)PROPER_1.39.0.zip(r-4.4)PROPER_1.39.0.zip(r-4.3)
PROPER_1.39.0.tgz(r-4.4-any)PROPER_1.39.0.tgz(r-4.3-any)
PROPER_1.39.0.tar.gz(r-4.5-noble)PROPER_1.39.0.tar.gz(r-4.4-noble)
PROPER_1.39.0.tgz(r-4.4-emscripten)PROPER_1.39.0.tgz(r-4.3-emscripten)
PROPER.pdf |PROPER.html✨
PROPER/json (API)
| # Install 'PROPER' in R: |
| install.packages('PROPER', repos = c('https://bioc.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-1.39.0(bioc 3.21)PROPER-1.38.0(bioc 3.20)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
immunooncologysequencingrnaseqdifferentialexpression
Last updated 2 months agofrom:57f641a309. Checks:OK: 1 WARNING: 6. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Nov 30 2024 |
| R-4.5-win | WARNING | Nov 30 2024 |
| R-4.5-linux | WARNING | Nov 30 2024 |
| R-4.4-win | WARNING | Nov 30 2024 |
| R-4.4-mac | WARNING | Nov 30 2024 |
| R-4.3-win | WARNING | Nov 30 2024 |
| R-4.3-mac | WARNING | Nov 30 2024 |
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 |
