consensusOV
Gene expression-based subtype classification for high-grade serous ovarian cancer
Bioconductor version: Release (3.19)
This package implements four major subtype classifiers for high-grade serous (HGS) ovarian cancer as described by Helland et al. (PLoS One, 2011), Bentink et al. (PLoS One, 2012), Verhaak et al. (J Clin Invest, 2013), and Konecny et al. (J Natl Cancer Inst, 2014). In addition, the package implements a consensus classifier, which consolidates and improves on the robustness of the proposed subtype classifiers, thereby providing reliable stratification of patients with HGS ovarian tumors of clearly defined subtype.
Author: Gregory M Chen [aut], Lavanya Kannan [aut], Ludwig Geistlinger [aut], Victor Kofia [aut], Levi Waldron [aut], Christopher Eeles [ctb], Benjamin Haibe-Kains [aut, cre]
Maintainer: Benjamin Haibe-Kains <benjamin.haibe.kains at utoronto.ca>
citation("consensusOV")):
Installation
To install this package, start R (version "4.4") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("consensusOV")
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("consensusOV")| Molecular subtyping for ovarian cancer | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Classification, Clustering, DifferentialExpression, GeneExpression, Microarray, Software, Transcriptomics |
| Version | 1.26.0 |
| In Bioconductor since | BioC 3.6 (R-3.4) (7 years) |
| License | Artistic-2.0 |
| Depends | R (>= 3.6) |
| Imports | Biobase, GSVA(>= 1.50.0), gdata, genefu, limma, matrixStats, randomForest, stats, utils, methods, BiocParallel |
| System Requirements | |
| URL | http://www.pmgenomics.ca/bhklab/software/consensusOV |
| Bug Reports | https://github.com/bhklab/consensusOV/issues |
See More
| Suggests | BiocStyle, ggplot2, knitr, rmarkdown, magick |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | signifinder |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | consensusOV_1.26.0.tar.gz |
| Windows Binary (x86_64) | consensusOV_1.26.0.zip |
| macOS Binary (x86_64) | consensusOV_1.26.0.tgz |
| macOS Binary (arm64) | consensusOV_1.26.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/consensusOV |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/consensusOV |
| Bioc Package Browser | https://code.bioconductor.org/browse/consensusOV/ |
| Package Short Url | https://bioconductor.org/packages/consensusOV/ |
| Package Downloads Report | Download Stats |