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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 (3.19)

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")

# 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 2.35.0
In Bioconductor since BioC 2.8 (R-2.13) (13 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
Linking To
Enhances
Depends On Me
Imports Me consensusOV, PDATK
Suggests Me breastCancerMAINZ, breastCancerNKI, breastCancerTRANSBIG, breastCancerUNT, breastCancerUPP, breastCancerVDX, GSgalgoR
Links To Me
Build Report Build Report

Package Archives

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

Source Package genefu_2.35.0.tar.gz
Windows Binary genefu_2.35.0.zip
macOS Binary (x86_64) genefu_2.35.0.tgz
macOS Binary (arm64)
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