To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("genefu")
In most cases, you don't need to download the package archive at all.
genefu
Relevant Functions for Gene Expression Analysis, Especially in Breast Cancer.
Bioconductor version: 3.0
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, survival analysis, ...
Author: Benjamin Haibe-Kains, Markus Schroeder, Gianluca Bontempi, Christos Sotiriou, John Quackenbush
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 and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("genefu")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("genefu")
| R Script | genefu An Introduction (HowTo) | |
| Reference Manual | ||
| Text | README |
Details
| biocViews | Classification, Clustering, DifferentialExpression, GeneExpression, Software, Visualization |
| Version | 1.16.0 |
| In Bioconductor since | BioC 2.8 (R-2.13) |
| License | Artistic-2.0 |
| Depends | survcomp, mclust, biomaRt, R (>= 2.10) |
| Imports | amap |
| LinkingTo | |
| Suggests | GeneMeta, breastCancerVDX, breastCancerMAINZ, breastCancerTRANSBIG, breastCancerUPP, breastCancerUNT, breastCancerNKI, rmeta, Biobase, xtable |
| SystemRequirements | |
| Enhances | |
| URL | http://www.pmgenomics.ca/bhklab/ |
| Depends On Me | |
| Imports Me | |
| Suggests Me | breastCancerMAINZ, breastCancerNKI, breastCancerTRANSBIG, breastCancerUNT, breastCancerUPP, breastCancerVDX |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | genefu_1.16.0.tar.gz |
| Windows Binary | genefu_1.16.0.zip |
| Mac OS X 10.6 (Snow Leopard) | genefu_1.16.0.tgz |
| Mac OS X 10.9 (Mavericks) | genefu_1.16.0.tgz |
| Browse/checkout source | (username/password: readonly) |
| Package Downloads Report | Download Stats |
Common Bioconductor workflows include:
- Oligonucleotide Arrays
- High-throughput Sequencing
- Counting Reads for Differential Expression (parathyroideSE vignette)
- Annotation
- Annotating Variants
- Annotating Ranges
- Flow Cytometry and other assays
- Candidate Binding Sites for Known Transcription Factors
- Cloud-enabled cis-eQTL search and annotation
- RNA-Seq workflow: gene-level exploratory analysis and differential expression
- Changing genomic coordinate systems with rtracklayer::liftOver
- Mass spectrometry and proteomics data analysis
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