genefu

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

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9, 3.8, 3.7, 3.6, 3.5, 3.4, 3.3, 3.2, 3.1, 3.0, 2.14, 2.13, 2.12, 2.11, 2.10, 2.9, 2.8

Computation of Gene Expression-Based Signatures in Breast Cancer

Bioconductor version: Development (3.24)

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], Jermiah Joseph [ctb], Benjamin Haibe-Kains [aut, cre]

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

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

Deena M.A. Gendoo, Natchar Ratanasirigulchai, Markus S. Schroeder, Laia Pare, Joel S Parker, Aleix Prat, Benjamin Haibe-Kains. genefu: Computation of Gene Expression-Based Signatures in Breast Cancer. doi:10.18129/B9.bioc.genefu, R package version 2.45.0, https://bioconductor.org/packages/genefu.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") and enter:

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

## The following initializes the development version of Bioconductor
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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	Classification, Clustering, DifferentialExpression, GeneExpression, Software, Visualization
Version	2.45.0
In Bioconductor since	BioC 2.8 (R-2.13) (15.5 years)
License	Artistic-2.0
Depends	R (>= 4.1), survcomp, biomaRt, iC10, AIMS
Imports	amap, impute, mclust, limma, graphics, stats, utils, iC10TrainingData
System Requirements
URL	http://www.pmgenomics.ca/bhklab/software/genefu

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, r-universe

Package Archives

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

Source Package	genefu_2.45.0.tar.gz
Windows Binary (x86_64)	genefu_2.45.0.zip
macOS Binary (big-sur-x86_64)	genefu_2.45.0.tgz
macOS Binary (sonoma-arm64)	genefu_2.45.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/genefu
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/genefu
Package Short Url	https://bioconductor.org/packages/genefu/
Package Downloads Report	Download Stats