Package: oncomix
Title: Identifying Genes Overexpressed in Subsets of Tumors from
        Tumor-Normal mRNA Expression Data
Version: 1.33.0
Author: Daniel Pique, John Greally, Jessica Mar
Maintainer: Daniel Pique <daniel.pique@med.einstein.yu.edu>
Description: 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.
Depends: R (>= 3.4.0)
License: GPL-3
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.0.1
Suggests: knitr, rmarkdown, testthat, RMySQL
Imports: ggplot2, ggrepel, RColorBrewer, mclust, stats,
        SummarizedExperiment
VignetteBuilder: knitr
biocViews: GeneExpression, Sequencing
Config/pak/sysreqs: zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2025-10-29 14:41:55 UTC
RemoteUrl: https://github.com/bioc/oncomix
RemoteRef: HEAD
RemoteSha: cca44aa290fa3f2f79a933f137c11757b84cb5fc
NeedsCompilation: no
Packaged: 2026-03-05 08:59:52 UTC; root
Built: R 4.6.0; ; 2026-03-05 09:01:19 UTC; windows
