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oncomix

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


Bioconductor version: Release (3.18)

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")):

Installation

To install this package, start R (version "4.3") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("oncomix")

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

Documentation

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

browseVignettes("oncomix")
OncoMix Vignette HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews GeneExpression, Sequencing, Software
Version 1.24.0
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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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package oncomix_1.24.0.tar.gz
Windows Binary oncomix_1.24.0.zip (64-bit only)
macOS Binary (x86_64) oncomix_1.24.0.tgz
macOS Binary (arm64) oncomix_1.24.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/oncomix
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/oncomix
Bioc Package Browser https://code.bioconductor.org/browse/oncomix/
Package Short Url https://bioconductor.org/packages/oncomix/
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