Package: iDOS 1.0.1
iDOS: Integrated Discovery of Oncogenic Signatures
A method to integrate molecular profiles of cancer patients (gene copy number and mRNA abundance) to identify candidate gain of function alterations. These candidate alterations can be subsequently further tested to discover cancer driver alterations. Briefly, this method tests of genomic correlates of mRNA dysregulation and prioritise those where DNA gains/amplifications are associated with elevated mRNA expression of the same gene. For details see, Haider S et al. (2016) "Genomic alterations underlie a pan-cancer metabolic shift associated with tumour hypoxia", Genome Biology, <https://pubmed.ncbi.nlm.nih.gov/27358048/>.
Authors:
iDOS_1.0.1.tar.gz
iDOS_1.0.1.zip(r-4.5)iDOS_1.0.1.zip(r-4.4)iDOS_1.0.1.zip(r-4.3)
iDOS_1.0.1.tgz(r-4.4-any)iDOS_1.0.1.tgz(r-4.3-any)
iDOS_1.0.1.tar.gz(r-4.5-noble)iDOS_1.0.1.tar.gz(r-4.4-noble)
iDOS_1.0.1.tgz(r-4.4-emscripten)iDOS_1.0.1.tgz(r-4.3-emscripten)
iDOS.pdf |iDOS.html✨
iDOS/json (API)
NEWS
| # Install 'iDOS' in R: |
| install.packages('iDOS', repos = c('https://syedhaider5.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 9 months agofrom:40b5f76f63. Checks:OK: 7. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Nov 07 2024 |
| R-4.5-win | OK | Nov 07 2024 |
| R-4.5-linux | OK | Nov 07 2024 |
| R-4.4-win | OK | Nov 07 2024 |
| R-4.4-mac | OK | Nov 07 2024 |
| R-4.3-win | OK | Nov 07 2024 |
| R-4.3-mac | OK | Nov 07 2024 |
Exports:create.counts.tablecreate.training.validation.splitestimate.expression.cna.correlationestimate.null.distribution.correlationfind.DE.featuresget.program.defaultsget.test.dataget.top.featuresload.datasets
Dependencies:formatRfutile.loggerfutile.optionslambda.rVennDiagram
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| create.counts.table | create.counts.table |
| create.training.validation.split | create.training.validation.split |
| estimate.expression.cna.correlation | estimate.expression.cna.correlation |
| estimate.null.distribution.correlation | estimate.null.distribution.correlation |
| find.DE.features | find.DE.features |
| get.program.defaults | get.program.defaults |
| get.test.data | get.test.data |
| get.top.features | get.top.features |
| load.datasets | load.datasets |
