genefu

DOI: 10.18129/B9.bioc.genefu    

Computation of Gene Expression-Based Signatures in Breast Cancer

Bioconductor version: Release (3.8)

Description: 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, Natchar Ratanasirigulchai, Markus S. Schroder, Laia Pare, Joel S. Parker, Aleix Prat, and Benjamin Haibe-Kains

Maintainer: Benjamin Haibe-Kains <benjamin.haibe.kains at utoronto.ca>, Markus Schroeder <markus.schroeder at ucdconnect.ie>

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

Installation

To install this package, start R (version "3.5") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("genefu", version = "3.8")

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")

 

PDF R Script genefu An Introduction (HowTo)
PDF   Reference Manual
Text   README

Details

biocViews Classification, Clustering, DifferentialExpression, GeneExpression, Software, Visualization
Version 2.14.0
In Bioconductor since BioC 2.8 (R-2.13) (7.5 years)
License Artistic-2.0
Depends survcomp, mclust, limma, biomaRt, iC10, AIMS, R (>= 2.10)
Imports amap
LinkingTo
Suggests GeneMeta, breastCancerVDX, breastCancerMAINZ, breastCancerTRANSBIG, breastCancerUPP, breastCancerUNT, breastCancerNKI, rmeta, Biobase, xtable, knitr, caret, survival
SystemRequirements
Enhances
URL http://www.pmgenomics.ca/bhklab/software/genefu
Depends On Me
Imports Me consensusOV
Suggests Me breastCancerMAINZ, breastCancerNKI, breastCancerTRANSBIG, breastCancerUNT, breastCancerUPP, breastCancerVDX
Links To Me
Build Report  

Package Archives

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

Source Package genefu_2.14.0.tar.gz
Windows Binary genefu_2.14.0.zip
Mac OS X 10.11 (El Capitan) genefu_2.14.0.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 http://bioconductor.org/packages/genefu/
Package Downloads Report Download Stats

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