Registration Open for Bioc2024
Early registration discount pricing ends May 31!

consensusOV

This is the development version of consensusOV; for the stable release version, see consensusOV.

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


Bioconductor version: Development (3.20)

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 (from within R, enter citation("consensusOV")):

Installation

To install this package, start R (version "4.4") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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 PDF
NEWS Text

Details

biocViews Classification, Clustering, DifferentialExpression, GeneExpression, Microarray, Software, Transcriptomics
Version 1.27.0
In Bioconductor since BioC 3.6 (R-3.4) (6.5 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
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_1.27.0.tar.gz
Windows Binary consensusOV_1.27.0.zip
macOS Binary (x86_64) consensusOV_1.27.0.tgz
macOS Binary (arm64) consensusOV_1.27.0.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