oncomix
Identifying Genes Overexpressed in Subsets of Tumors from Tumor-Normal mRNA Expression Data
Bioconductor version: Release (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 med.einstein.yu.edu>
citation("oncomix")
):
Installation
To install this package, start R (version "4.4") 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 | ||
NEWS | Text |
Details
biocViews | GeneExpression, Sequencing, Software |
Version | 1.28.0 |
In Bioconductor since | BioC 3.6 (R-3.4) (7 years) |
License | GPL-3 |
Depends | R (>= 3.4.0) |
Imports | ggplot2, ggrepel, RColorBrewer, mclust, stats, SummarizedExperiment |
System Requirements | |
URL |
See More
Suggests | knitr, rmarkdown, testthat, RMySQL |
Linking To | |
Enhances | |
Depends On Me | |
Imports Me | |
Suggests Me | |
Links To Me | |
Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
Source Package | oncomix_1.28.0.tar.gz |
Windows Binary (x86_64) | oncomix_1.28.0.zip |
macOS Binary (x86_64) | oncomix_1.28.0.tgz |
macOS Binary (arm64) | oncomix_1.27.0.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/ |
Package Downloads Report | Download Stats |