Package: GRAPE 0.1.1
GRAPE: Gene-Ranking Analysis of Pathway Expression
Gene-Ranking Analysis of Pathway Expression (GRAPE) is a tool for summarizing the consensus behavior of biological pathways in the form of a template, and for quantifying the extent to which individual samples deviate from the template. GRAPE templates are based only on the relative rankings of the genes within the pathway and can be used for classification of tissue types or disease subtypes. GRAPE can be used to represent gene-expression samples as vectors of pathway scores, where each pathway score indicates the departure from a given collection of reference samples. The resulting pathway- space representation can be used as the feature set for various applications, including survival analysis and drug-response prediction. Users of GRAPE should use the following citation: Klein MI, Stern DF, and Zhao H. GRAPE: A pathway template method to characterize tissue-specific functionality from gene expression profiles. BMC Bioinformatics, 18:317 (June 2017).
Authors:
GRAPE_0.1.1.tar.gz
GRAPE_0.1.1.zip(r-4.7)GRAPE_0.1.1.zip(r-4.6)GRAPE_0.1.1.zip(r-4.5)
GRAPE_0.1.1.tgz(r-4.6-any)GRAPE_0.1.1.tgz(r-4.5-any)
GRAPE_0.1.1.tar.gz(r-4.7-any)GRAPE_0.1.1.tar.gz(r-4.6-any)
GRAPE_0.1.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
GRAPE/json (API)
| # Install 'GRAPE' in R: |
| install.packages('GRAPE', repos = c('https://michaelklein916.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 from:a2f2f92bdc. Checks:9 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel-x86_64 | OK | 83 | ||
| source / vignettes | OK | 162 | ||
| linux-release-x86_64 | OK | 90 | ||
| macos-release-arm64 | OK | 75 | ||
| macos-oldrel-arm64 | OK | 98 | ||
| windows-devel | OK | 71 | ||
| windows-release | OK | 80 | ||
| windows-oldrel | OK | 81 | ||
| wasm-release | OK | 87 |
Exports:getPathwayScoresmakeBinaryTemplateAndProbabilityTemplatemakeGRAPE_psMatmakePairwiseOrdermakePairwiseOrderNamespredictClassDIRACpredictClassGRAPEpredictClassPCw_quad
Dependencies:
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Calculate Pathway Scores | getPathwayScores |
| Make binary template and probability template | makeBinaryTemplateAndProbabilityTemplate |
| Calculate Pathway Space Matrix | makeGRAPE_psMat |
| Make pairwise order representation of a sample | makePairwiseOrder |
| Make template names from gene names | makePairwiseOrderNames |
| DIRAC Classification | predictClassDIRAC |
| GRAPE Classification | predictClassGRAPE |
| PC Classification | predictClassPC |
| Quadratic weight function | w_quad |
