Package: sigsquared 1.45.0
UnJin Lee
sigsquared: Gene signature generation for functionally validated signaling pathways
By leveraging statistical properties (log-rank test for survival) of patient cohorts defined by binary thresholds, poor-prognosis patients are identified by the sigsquared package via optimization over a cost function reducing type I and II error.
Authors:
sigsquared_1.45.0.tar.gz
sigsquared_1.45.0.zip(r-4.7)sigsquared_1.45.0.zip(r-4.6)sigsquared_1.45.0.zip(r-4.5)
sigsquared_1.45.0.tgz(r-4.6-any)sigsquared_1.45.0.tgz(r-4.5-any)
sigsquared_1.45.0.tar.gz(r-4.7-any)sigsquared_1.45.0.tar.gz(r-4.6-any)
sigsquared_1.45.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
sigsquared/json (API)
| # Install 'sigsquared' in R: |
| install.packages('sigsquared', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Datasets:
- BrCa443 - Breast Cancer 443 Data Set
On BioConductor:sigsquared-1.45.0(bioc 3.24)sigsquared-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.
Last updated from:37ea3e2fe0. Checks:1 ERROR, 7 NOTE, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | ERROR | 129 | ||
| linux-devel-x86_64 | NOTE | 172 | ||
| source / vignettes | OK | 174 | ||
| linux-release-x86_64 | NOTE | 164 | ||
| macos-release-arm64 | NOTE | 119 | ||
| macos-oldrel-arm64 | NOTE | 91 | ||
| windows-devel | NOTE | 102 | ||
| windows-release | NOTE | 91 | ||
| windows-oldrel | NOTE | 90 | ||
| wasm-release | OK | 91 |
Exports:analysisPipelineensembleAdjustablegetDirectgetGenesgetNGenesgetThresholdssetDirectsetGenessetGeneSignaturesetThresholds
Dependencies:BiobaseBiocGenericsgenericslatticeMatrixsurvival
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Training of thresholds | analysisPipeline |
| Breast Cancer 443 Data Set | BrCa443 |
| Application of geneSignature object | ensembleAdjustable |
| Class '"geneSignature"' | analysisPipeline,ExpressionSet,geneSignature-method ensembleAdjustable,ExpressionSet,geneSignature-method ensembleAdjustable,matrix,geneSignature-method geneSignature-class getDirect,geneSignature-method getGenes,geneSignature-method getGenes,solnSpace-method getNGenes,geneSignature-method getThresholds,geneSignature-method getThresholds,solnSpace-method setDirect,geneSignature,numeric-method setGenes,geneSignature-method setGenes,solnSpace-method setGeneSignature,geneSignature-method setThresholds,geneSignature-method setThresholds,solnSpace-method |
| geneSignature functions | getDirect getGenes getNGenes getThresholds setDirect setGenes setGeneSignature setThresholds |
| The sigsquared package | sigsquared |
