oncomix
This is the released version of oncomix; for the devel version, see oncomix.
Identifying Genes Overexpressed in Subsets of Tumors from Tumor-Normal mRNA Expression Data
Bioconductor version: Release (3.23)
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")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") 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 | 1.34.0 |
| In Bioconductor since | BioC 3.6 (R-3.4) (9 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_1.34.0.tar.gz |
| Windows Binary (x86_64) | oncomix_1.34.0.zip |
| macOS Binary (big-sur-x86_64) | oncomix_1.34.0.tgz |
| macOS Binary (sonoma-arm64) | oncomix_1.34.0.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 |