consensusOV

DOI: 10.18129/B9.bioc.consensusOV  

Gene expression-based subtype classification for high-grade serous ovarian cancer

Bioconductor version: Release (3.16)

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, Lavanya Kannan, Ludwig Geistlinger, Victor Kofia, Levi Waldron, Benjamin Haibe-Kains

Maintainer: Benjamin Haibe-Kains <benjamin.haibe.kains at utoronto.ca>

Installation

To install this package, start R (version "4.2") 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")

 

HTML	R Script	Molecular subtyping for ovarian cancer
PDF		Reference Manual
Text		NEWS

Details

biocViews	Classification, Clustering, DifferentialExpression, GeneExpression, Microarray, Software, Transcriptomics
Version	1.20.0
In Bioconductor since	BioC 3.6 (R-3.4) (5.5 years)
License	Artistic-2.0
Depends	R (>= 3.6)
Imports	Biobase, GSVA, gdata, genefu, limma, matrixStats, randomForest, stats, utils, methods
LinkingTo
Suggests	BiocStyle, ggplot2, knitr, rmarkdown
SystemRequirements
Enhances
URL	http://www.pmgenomics.ca/bhklab/software/consensusOV
BugReports	https://github.com/bhklab/consensusOV/issues
Depends On Me
Imports Me	signifinder
Suggests Me
Links To Me
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	consensusOV_1.20.0.tar.gz
Windows Binary	consensusOV_1.20.0.zip
macOS Binary (x86_64)	consensusOV_1.20.0.tgz
macOS Binary (arm64)	consensusOV_1.20.0.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