oncomix

DOI: 10.18129/B9.bioc.oncomix    

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

Bioconductor version: Release (3.7)

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 and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("oncomix")

Documentation

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

browseVignettes("oncomix")

 

HTML R Script OncoMix Vignette
PDF   Reference Manual
Text   NEWS

Details

biocViews GeneExpression, Sequencing, Software
Version 1.2.0
License GPL-3
Depends R (>= 3.4.0)
Imports ggplot2, ggrepel, RColorBrewer, mclust, stats, SummarizedExperiment
LinkingTo
Suggests knitr, rmarkdown, testthat, RMySQL
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report  

Package Archives

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

Source Package oncomix_1.2.0.tar.gz
Windows Binary oncomix_1.2.0.zip
Mac OS X 10.11 (El Capitan) oncomix_1.2.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/oncomix
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/oncomix
Package Short Url http://bioconductor.org/packages/oncomix/
Package Downloads Report Download Stats

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