1. Introduction | 1.1 Motivation for Developing Oncomix | 1.2 Distribution of Oncogene mRNA Expression | 1.3 Comparison of Oncomix to Existing Differential Expression Methods | 2. Identifying Oncogene Candidates | 2.1 Loading Example Data and Exploring the mixModelParams Object | 2.2 Selecting Genes that Appear Most Like the Idealized Oncogene | 3. Visualize the Output | 3.1 Visualize Isoforms with a High SI & Oncomix Score | 3.2 Visualize the Distribution of Isoforms that Map to Known Oncogenes | 3.3 Visualize the Distribution of the Oncomix Score | 4. Session Info
Package: oncomix 1.35.0
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:
oncomix_1.35.0.tar.gz
oncomix_1.35.0.zip(r-4.7)oncomix_1.35.0.zip(r-4.6)oncomix_1.35.0.zip(r-4.5)
oncomix_1.35.0.tgz(r-4.6-any)oncomix_1.35.0.tgz(r-4.5-any)
oncomix_1.35.0.tar.gz(r-4.7-any)oncomix_1.35.0.tar.gz(r-4.6-any)
oncomix_1.35.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
oncomix/json (API)
| # Install 'oncomix' in R: |
| install.packages('oncomix', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Datasets:
- 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-1.35.0(bioc 3.24)oncomix-1.34.0(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:9760062b4e. Checks:1 ERROR, 7 NOTE, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | ERROR | 178 | ||
| linux-devel-x86_64 | NOTE | 313 | ||
| source / vignettes | OK | 224 | ||
| linux-release-x86_64 | NOTE | 269 | ||
| macos-release-arm64 | NOTE | 149 | ||
| macos-oldrel-arm64 | NOTE | 144 | ||
| windows-devel | NOTE | 194 | ||
| windows-release | NOTE | 205 | ||
| windows-oldrel | NOTE | 195 | ||
| wasm-release | OK | 152 |
Exports:mixModelParamsoncoMixBimodaloncoMixIdealoncoMixTraditionalDEplotGeneHistscatterMixPlottoMatrixtopGeneQuants
Dependencies:abindBiobaseBiocGenericsclicpp11DelayedArrayfarvergenericsGenomicRangesggplot2ggrepelgluegtableIRangesisobandlabelinglatticelifecycleMatrixMatrixGenericsmatrixStatsmclustR6RColorBrewerRcpprlangS4ArraysS4VectorsS7scalesSeqinfoSparseArraySummarizedExperimentvctrsviridisLitewithrXVector
