DOI: 10.18129/B9.bioc.oncomix  

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see oncomix.

Identifying Genes Overexpressed in Subsets of Tumors from Tumor-Normal mRNA Expression Data

Bioconductor version: 3.16

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.

Author: Daniel Pique, John Greally, Jessica Mar

Maintainer: Daniel Pique <daniel.pique at med.einstein.yu.edu>

Citation (from within R, enter citation("oncomix")):


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biocViews GeneExpression, Sequencing, Software
Version 1.20.0
In Bioconductor since BioC 3.6 (R-3.4) (5.5 years)
License GPL-3
Depends R (>= 3.4.0)
Imports ggplot2, ggrepel, RColorBrewer, mclust, stats, SummarizedExperiment
Suggests knitr, rmarkdown, testthat, RMySQL
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