genefu

Computation of Gene Expression-Based Signatures in Breast Cancer


Bioconductor version: Release (3.20)

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 "4.4") and enter:


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

BiocManager::install("genefu")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

Reference Manual PDF
NEWS Text

Details

biocViews Classification, Clustering, DifferentialExpression, GeneExpression, Software, Visualization
Version 2.37.0
In Bioconductor since BioC 2.8 (R-2.13) (13.5 years)
License Artistic-2.0
Depends R (>= 4.1), survcomp, biomaRt, iC10, AIMS
Imports amap, impute, mclust, limma, graphics, stats, utils
System Requirements
URL http://www.pmgenomics.ca/bhklab/software/genefu
See More
Suggests GeneMeta, breastCancerVDX, breastCancerMAINZ, breastCancerTRANSBIG, breastCancerUPP, breastCancerUNT, breastCancerNKI, rmeta, Biobase, xtable, knitr, caret, survival, BiocStyle, magick, rmarkdown
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Package Archives

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

Source Package
Windows Binary (x86_64)
macOS Binary (x86_64)
macOS Binary (arm64) genefu_2.37.0.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/
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