genefu

DOI: 10.18129/B9.bioc.genefu  

Computation of Gene Expression-Based Signatures in Breast Cancer

Bioconductor version: Release (3.16)

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>

Installation

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

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("genefu")

 

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

Details

biocViews	Classification, Clustering, DifferentialExpression, GeneExpression, Software, Visualization
Version	2.30.0
In Bioconductor since	BioC 2.8 (R-2.13) (12 years)
License	Artistic-2.0
Depends	R (>= 4.1), survcomp, biomaRt, iC10, AIMS
Imports	amap, impute, mclust, limma, graphics, stats, utils
LinkingTo
Suggests	GeneMeta, breastCancerVDX, breastCancerMAINZ, breastCancerTRANSBIG, breastCancerUPP, breastCancerUNT, breastCancerNKI, rmeta, Biobase, xtable, knitr, caret, survival, BiocStyle, magick, rmarkdown
SystemRequirements
Enhances
URL	http://www.pmgenomics.ca/bhklab/software/genefu
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_2.30.0.tar.gz
Windows Binary	genefu_2.30.0.zip (64-bit only)
macOS Binary (x86_64)	genefu_2.30.0.tgz
macOS Binary (arm64)	genefu_2.30.0.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