To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("safe")
In most cases, you don't need to download the package archive at all.
safe
|
This package is for version 3.2 of Bioconductor; for the stable, up-to-date release version, see safe.
Significance Analysis of Function and Expression
Bioconductor version: 3.2
SAFE is a resampling-based method for testing functional categories in gene expression experiments. SAFE can be applied to 2-sample and multi-class comparisons, or simple linear regressions. Other experimental designs can also be accommodated through user-defined functions.
Author: William T. Barry
Maintainer: William T. Barry <bbarry at jimmy.harvard.edu>
Citation (from within R,
enter citation("safe")):
Installation
To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("safe")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("safe")
| SAFE manual | ||
| Reference Manual |
Details
| biocViews | DifferentialExpression, GeneSetEnrichment, Pathways, Software, StatisticalMethod |
| Version | 3.10.0 |
| In Bioconductor since | BioC 1.6 (R-2.1) or earlier (> 11 years) |
| License | GPL (>= 2) |
| Depends | R (>= 2.4.0), AnnotationDbi, Biobase, methods, SparseM |
| Imports | |
| LinkingTo | |
| Suggests | GO.db, PFAM.db, reactome.db, hgu133a.db, breastCancerUPP, survival, foreach, doRNG, Rgraphviz, GOstats |
| SystemRequirements | |
| Enhances | |
| URL | |
| Depends On Me | |
| Imports Me | EnrichmentBrowser |
| Suggests Me | |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | safe_3.10.0.tar.gz |
| Windows Binary | safe_3.10.0.zip |
| Mac OS X 10.6 (Snow Leopard) | safe_3.10.0.tgz |
| Mac OS X 10.9 (Mavericks) | safe_3.10.0.tgz |
| Subversion source | (username/password: readonly) |
| Git source | https://github.com/Bioconductor-mirror/safe/tree/release-3.2 |
| Package Short Url | http://bioconductor.org/packages/safe/ |
| Package Downloads Report | Download Stats |
Documentation »
Bioconductor
- Package vignettes and manuals.
- Workflows for learning and use.
- Course and conference material.
- Videos.
- Community resources and tutorials.
R / CRAN packages and documentation
Support »
Please read the posting guide. Post questions about Bioconductor to one of the following locations:
- Support site - for questions about Bioconductor packages
- Bioc-devel mailing list - for package developers
