Package: samr 3.0
samr: SAM: Significance Analysis of Microarrays
Significance Analysis of Microarrays for differential expression analysis, RNAseq data and related problems.
Authors:
samr_3.0.tar.gz
samr_3.0.zip(r-4.5)samr_3.0.zip(r-4.4)samr_3.0.zip(r-4.3)
samr_3.0.tgz(r-4.4-x86_64)samr_3.0.tgz(r-4.4-arm64)samr_3.0.tgz(r-4.3-x86_64)samr_3.0.tgz(r-4.3-arm64)
samr_3.0.tar.gz(r-4.5-noble)samr_3.0.tar.gz(r-4.4-noble)
samr_3.0.tgz(r-4.4-emscripten)samr_3.0.tgz(r-4.3-emscripten)
samr.pdf |samr.html✨
samr/json (API)
| # Install 'samr' in R: |
| install.packages('samr', repos = c('https://tibshirani.r-universe.dev', 'https://cloud.r-project.org')) |
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated 6 years agofrom:bf0d63f2bc. Checks:OK: 1 NOTE: 8. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Oct 31 2024 |
| R-4.5-win-x86_64 | NOTE | Oct 31 2024 |
| R-4.5-linux-x86_64 | NOTE | Oct 31 2024 |
| R-4.4-win-x86_64 | NOTE | Oct 31 2024 |
| R-4.4-mac-x86_64 | NOTE | Oct 31 2024 |
| R-4.4-mac-aarch64 | NOTE | Oct 31 2024 |
| R-4.3-win-x86_64 | NOTE | Oct 31 2024 |
| R-4.3-mac-x86_64 | NOTE | Oct 31 2024 |
| R-4.3-mac-aarch64 | NOTE | Oct 31 2024 |
Exports:check.formatplot.SAMoutputprint.SAMoutputquantitative.funcrunSAMSAMsamrsamr.assess.samplesizesamr.assess.samplesize.plotsamr.compute.delta.tablesamr.compute.siggenes.tablesamr.const.multiclass.responsesamr.const.oneclass.responsesamr.const.oneclass.timecourse.responsesamr.const.patterndiscovery.responsesamr.const.quantitative.responsesamr.const.survival.responsesamr.const.twoclass.paired.responsesamr.const.twoclass.paired.timecourse.responsesamr.const.twoclass.unpaired.responsesamr.const.twoclass.unpaired.timecourse.responsesamr.estimate.depthsamr.missratesamr.norm.datasamr.plotsamr.pvalues.from.permssamr.tail.strengthSAMseqttest.func
Dependencies:base64encbslibcachemclicommonmarkcrayondigestfansifastmapfontawesomefsglueGSAhtmltoolshttpuvimputejquerylibjsonlitelaterlifecyclemagrittrmatrixStatsmemoisemimeopenxlsxpillarpkgconfigpromisesR6rappdirsRcpprlangsassshinyshinyFilessourcetoolsstringitibbleutf8vctrswithrxtablezip
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Run the sam webapp | runSAM |
| Significance analysis of microarrays - simple user interface | SAM |
| Significance analysis of microarrays | samr |
| Assess the sample size for a SAM analysis | samr.assess.samplesize |
| Make a plot of the results from samr.assess.samplesize | samr.assess.samplesize.plot |
| Compute delta table for SAM analysis | samr.compute.delta.table |
| Compute significant genes table | samr.compute.siggenes.table |
| estimate the sequencing depth | samr.estimate.depth |
| Estimate the miss rate table for a SAM analysis | samr.missrate |
| output normalized sequencing data | samr.norm.data |
| Make Q-Q plot for SAM analysis | samr.plot |
| Report estimated p-values for each gene, from a SAM analysis | samr.pvalues.from.perms |
| Estimate tail strength for a dataset, from a SAM analysis | samr.tail.strength |
| Significance analysis of sequencing data - simple user interface | SAMseq |
