oncomix

DOI: 10.18129/B9.bioc.oncomix    

This package is for version 3.9 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: 3.9

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>

Installation

To install this package, start R (version "3.6") and enter:

if (!requireNamespace("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")

 

HTML	R Script	OncoMix Vignette
PDF		Reference Manual
Text		NEWS

Details

biocViews	GeneExpression, Sequencing, Software
Version	1.6.0
In Bioconductor since	BioC 3.6 (R-3.4) (2 years)
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_1.6.0.tar.gz
Windows Binary	oncomix_1.6.0.zip
Mac OS X 10.11 (El Capitan)	oncomix_1.6.0.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	https://bioconductor.org/packages/oncomix/
Package Downloads Report	Download Stats