This site is a development preview. As such the content and styling may not be final and is subject to change before going into production. To see more information about the redesign click here.

Menu

Documentation:

R / CRAN packages and documentation

Support

Please read the posting guide. Post questions about Bioconductor to one of the following locations:

genefu

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

Computation of Gene Expression-Based Signatures in Breast Cancer

Bioconductor version: Development (3.18)

This package contains functions implementing various tasks usually required by gene expression analysis, especially in breast cancer studies: gene mapping between different microarray platforms, identification of molecular subtypes, implementation of published gene signatures, gene selection, and survival analysis.

Author: Deena M.A. Gendoo [aut], Natchar Ratanasirigulchai [aut], Markus S. Schroeder [aut], Laia Pare [aut], Joel S Parker [aut], Aleix Prat [aut], Nikta Feizi [ctb], Christopher Eeles [ctb], Benjamin Haibe-Kains [aut, cre]

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

Citation (from within R, enter citation("genefu")):

Installation

To install this package, start R (version "4.3") and enter: 

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

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

BiocManager::install("genefu")

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("genefu")
genefu: A Package For Breast Cancer Gene Expression Analysis HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews Classification, Clustering, DifferentialExpression, GeneExpression, Software, Visualization
Version 2.33.0
In Bioconductor since BioC 2.8 (R-2.13) (12.5 years)
License Artistic-2.0
Depends R (>= 4.1), survcomp, biomaRt, iC10, AIMS
Imports amap, impute, mclust, limma, graphics, stats, utils
Linking To
Suggests GeneMeta, breastCancerVDX, breastCancerMAINZ, breastCancerTRANSBIG, breastCancerUPP, breastCancerUNT, breastCancerNKI, rmeta, Biobase, xtable, knitr, caret, survival, BiocStyle, magick, rmarkdown
System Requirements
Enhances
URL http://www.pmgenomics.ca/bhklab/software/genefu
See More
Depends On Me
Imports Me consensusOV, PDATK
Suggests Me breastCancerMAINZ, breastCancerNKI, breastCancerTRANSBIG, breastCancerUNT, breastCancerUPP, breastCancerVDX, GSgalgoR
Links To Me
Build Report  

Package Archives

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

Source Package genefu_2.33.0.tar.gz
Windows Binary genefu_2.33.0.zip (64-bit only)
macOS Binary (x86_64) genefu_2.33.0.tgz
macOS Binary (arm64) genefu_2.33.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/genefu
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/genefu
Bioc Package Browser https://code.bioconductor.org/browse/genefu/
Package Short Url https://bioconductor.org/packages/genefu/
Package Downloads Report Download Stats