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>
citation("oncomix")):
Installation
To install this package, start R (version "3.6") 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 | 1.6.0 |
| 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 | |
| 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_1.6.0.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 |
| Bioc Package Browser | https://code.bioconductor.org/browse/oncomix/ |
| Package Short Url | https://bioconductor.org/packages/oncomix/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.9 | Source Archive |