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genefu

Computation of Gene Expression-Based Signatures in Breast Cancer

Bioconductor version: 3.24 · Package version: 2.45.0

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.

Installation

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

BiocManager::install("genefu")

Details

MaintainerBenjamin Haibe-Kains <benjamin.haibe.kains@utoronto.ca>
AuthorDeena 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]
LicenseArtistic-2.0
URLhttp://www.pmgenomics.ca/bhklab/software/genefu
Downloads rank1112
Source branchdevel
biocViewsClassification, Clustering, DifferentialExpression, GeneExpression, Software, Visualization

Documentation

Download

Follow the installation instructions to use this package in your R session.

Source packagegenefu_2.45.0.tar.gz
Windows binary (x86_64)genefu_2.45.0.zip
macOS binary (arm64)genefu_2.45.0.tgz
macOS binary (x86_64)genefu_2.45.0.tgz
Dependencies

Depends: R (>= 4.1), survcomp, biomaRt, iC10, AIMS

Imports: amap, impute, mclust, limma, graphics, stats, utils, iC10TrainingData

Suggests: GeneMeta, breastCancerVDX, breastCancerMAINZ, breastCancerTRANSBIG, breastCancerUPP, breastCancerUNT, breastCancerNKI, rmeta, Biobase, xtable, knitr, caret, survival, BiocStyle, magick, rmarkdown

Reverse dependencies

Imports Me (2): consensusOV, PDATK

Suggests Me (7): breastCancerMAINZ, breastCancerNKI, breastCancerTRANSBIG, breastCancerUNT, breastCancerUPP, breastCancerVDX, GSgalgoR