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This is the development version of oncomix; for the stable release version, see oncomix.

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

Bioconductor version: Development (3.20)

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>

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


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))

# The following initializes usage of Bioc devel


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

OncoMix Vignette HTML R Script
Reference Manual PDF


biocViews GeneExpression, Sequencing, Software
Version 1.27.0
In Bioconductor since BioC 3.6 (R-3.4) (6.5 years)
License GPL-3
Depends R (>= 3.4.0)
Imports ggplot2, ggrepel, RColorBrewer, mclust, stats, SummarizedExperiment
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Suggests knitr, rmarkdown, testthat, RMySQL
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Source Package oncomix_1.27.0.tar.gz
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