Package: oncomix 1.29.0
Daniel Pique
oncomix: Identifying Genes Overexpressed in Subsets of Tumors from Tumor-Normal mRNA Expression Data
This package helps identify mRNAs that are overexpressed in subsets of tumors relative to normal tissue. Ideal inputs would be paired tumor-normal data from the same tissue from many patients (>15 pairs). This unsupervised approach relies on the observation that oncogenes are characteristically overexpressed in only a subset of tumors in the population, and may help identify oncogene candidates purely based on differences in mRNA expression between previously unknown subtypes.
Authors:
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oncomix.pdf |oncomix.html✨
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NEWS
| # Install 'oncomix' in R: |
| install.packages('oncomix', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
- exprNmlIsof - Human Breast Cancer RNA-sequencing data from TCGA - Adj. Normal Tissue
- exprTumIsof - Human Breast Cancer RNA-sequencing data from TCGA - Tumor Tissue
- queryRes - Oncogene Database Mapping Gene Symbol to UCSC ID
On BioConductor:oncomix-1.29.0(bioc 3.21)oncomix-1.28.0(bioc 3.20)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated 2 months agofrom:34c2f12980. Checks:OK: 1 NOTE: 6. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Nov 29 2024 |
| R-4.5-win | NOTE | Nov 29 2024 |
| R-4.5-linux | NOTE | Nov 29 2024 |
| R-4.4-win | NOTE | Nov 29 2024 |
| R-4.4-mac | NOTE | Nov 29 2024 |
| R-4.3-win | NOTE | Nov 29 2024 |
| R-4.3-mac | NOTE | Nov 29 2024 |
Exports:mixModelParamsoncoMixBimodaloncoMixIdealoncoMixTraditionalDEplotGeneHistscatterMixPlottoMatrixtopGeneQuants
Dependencies:abindaskpassBiobaseBiocGenericsclicolorspacecrayoncurlDelayedArrayfansifarvergenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesggplot2ggrepelgluegtablehttrIRangesisobandjsonlitelabelinglatticelifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmclustmgcvmimemunsellnlmeopensslpillarpkgconfigR6RColorBrewerRcpprlangS4ArraysS4VectorsscalesSparseArraySummarizedExperimentsystibbleUCSC.utilsutf8vctrsviridisLitewithrXVectorzlibbioc
