genefu
Computation of Gene Expression-Based Signatures in Breast Cancer
Bioconductor version: Release (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("genefu")):
Installation
To install this package, start R (version "4.4") 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")| genefu: A Package For Breast Cancer Gene Expression Analysis | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Classification, Clustering, DifferentialExpression, GeneExpression, Software, Visualization |
| Version | 2.36.0 |
| In Bioconductor since | BioC 2.8 (R-2.13) (13.5 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 | PDATK, consensusOV |
| Suggests Me | GSgalgoR, breastCancerMAINZ, breastCancerNKI, breastCancerTRANSBIG, breastCancerUNT, breastCancerUPP, breastCancerVDX |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | genefu_2.36.0.tar.gz |
| Windows Binary (x86_64) | genefu_2.36.0.zip |
| macOS Binary (x86_64) | genefu_2.36.0.tgz |
| macOS Binary (arm64) | genefu_2.36.0.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 |