Bioconductor version: Release (3.17)
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: Ludwig Geistlinger <ludwig.geistlinger at gmail.com>
Citation (from within R,
enter citation("safe")
):
To install this package, start R (version "4.3") and enter:
if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("safe")
For older versions of R, please refer to the appropriate Bioconductor release.
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("safe")
R Script | SAFE manual | |
Reference Manual |
biocViews | DifferentialExpression, GeneSetEnrichment, Pathways, Software, StatisticalMethod |
Version | 3.40.1 |
In Bioconductor since | BioC 1.6 (R-2.1) or earlier (> 18.5 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 | EGSEA, EnrichmentBrowser |
Suggests Me | |
Links To Me | |
Build Report |
Follow Installation instructions to use this package in your R session.
Source Package | safe_3.40.1.tar.gz |
Windows Binary | safe_3.40.1.zip |
macOS Binary (x86_64) | safe_3.40.1.tgz |
macOS Binary (arm64) | safe_3.40.1.tgz |
Source Repository | git clone https://git.bioconductor.org/packages/safe |
Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/safe |
Bioc Package Browser | https://code.bioconductor.org/browse/safe/ |
Package Short Url | https://bioconductor.org/packages/safe/ |
Package Downloads Report | Download Stats |
Old Source Packages for BioC 3.17 | Source Archive |
Documentation »
Bioconductor
R / CRAN packages and documentation
Support »
Please read the posting guide. Post questions about Bioconductor to one of the following locations: