oncomix

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 (3.19)

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 "4.4") and enter:


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("oncomix")

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

Documentation


Reference Manual	PDF

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	GeneExpression, Sequencing, Software
Version	1.25.0
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
System Requirements
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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
Windows Binary
macOS Binary (x86_64)
macOS Binary (arm64)
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