genefu
This is the released version of genefu; for the devel version, see genefu.
Computation of Gene Expression-Based Signatures in Breast Cancer
Bioconductor version: Release (3.23)
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("genefu")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") 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 | 2.44.0 |
| 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 |
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 | consensusOV, PDATK |
| 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_2.44.0.tar.gz |
| Windows Binary (x86_64) | genefu_2.44.0.zip |
| macOS Binary (big-sur-x86_64) | genefu_2.44.0.tgz |
| macOS Binary (sonoma-arm64) | genefu_2.44.0.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 |