Introduction | Algorithm overview | Input data | Preprocessing | Differential expression testing | Visualization | References
Package: ROTS 2.5.1
Tomi Suomi
ROTS: Reproducibility-Optimized Test Statistic
Calculates the Reproducibility-Optimized Test Statistic (ROTS) for differential testing in omics data.
Authors:
ROTS_2.5.1.tar.gz
ROTS_2.5.1.zip(r-4.7)ROTS_2.5.1.zip(r-4.6)ROTS_2.5.1.zip(r-4.5)
ROTS_2.5.1.tgz(r-4.6-x86_64)ROTS_2.5.1.tgz(r-4.6-arm64)ROTS_2.5.1.tgz(r-4.5-x86_64)ROTS_2.5.1.tgz(r-4.5-arm64)
ROTS_2.5.1.tar.gz(r-4.7-arm64)ROTS_2.5.1.tar.gz(r-4.7-x86_64)ROTS_2.5.1.tar.gz(r-4.6-arm64)ROTS_2.5.1.tar.gz(r-4.6-x86_64)
ROTS_2.5.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
ROTS/json (API)
| # Install 'ROTS' in R: |
| install.packages('ROTS', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Datasets:
- affySpikeIn - Gene expression data from the Affymetrix spike-in experiment
- affySpikeIn.gnames - Gene expression data from the Affymetrix spike-in experiment
- affySpikeIn.L - Gene expression data from the Affymetrix spike-in experiment
- spikedgene - Gene expression data from the Affymetrix spike-in experiment
- upsSpikeIn - Protein expression data from the CPTAC Technology Assessment
On BioConductor:ROTS-2.5.1(bioc 3.24)ROTS-2.4.0(bioc 3.23)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
softwaregeneexpressiondifferentialexpressionmicroarrayrnaseqproteomicsimmunooncologycpp
Last updated from:cce4fb4304. Checks:1 ERROR, 13 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | ERROR | 178 | ||
| linux-devel-arm64 | OK | 199 | ||
| linux-devel-x86_64 | OK | 259 | ||
| source / vignettes | OK | 254 | ||
| linux-release-arm64 | OK | 199 | ||
| linux-release-x86_64 | OK | 258 | ||
| macos-release-arm64 | OK | 164 | ||
| macos-release-x86_64 | OK | 210 | ||
| macos-oldrel-arm64 | OK | 214 | ||
| macos-oldrel-x86_64 | OK | 355 | ||
| windows-devel | OK | 167 | ||
| windows-release | OK | 215 | ||
| windows-oldrel | OK | 178 | ||
| wasm-release | OK | 133 |
Exports:coxphROTSlmeROTSlmROTSresultsROTS
Dependencies:BHBiobaseBiocGenericsBiocParallelbootcodetoolscpp11formatRfutile.loggerfutile.optionsgenericslambda.rlatticelme4MASSMatrixminqanlmenloptrrbibutilsRcppRcppEigenRdpackreformulasrlangsnowsurvival
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Gene expression data from the Affymetrix spike-in experiment | affySpikeIn affySpikeIn.gnames affySpikeIn.L spikedgene |
| Reproducibility-Optimized Test Statistic (ROTS) | coxphROTS |
| Reproducibility-Optimized Test Statistic (ROTS) | lmeROTS |
| Reproducibility-Optimized Test Statistic (ROTS) | lmROTS |
| Plotting of a regROTS object | plot.regROTS |
| Plotting of a ROTS object | plot.ROTS |
| Gathering results from a regROTS object | results |
| Reproducibility-Optimized Test Statistic (ROTS) | ROTS-package print.ROTS ROTS |
| Summary of a regROTS object | summary.regROTS |
| Summary of a ROTS object | summary.ROTS |
| Protein expression data from the CPTAC Technology Assessment (Study 6) | upsSpikeIn |
