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Significance Analysis of Function and Expression

Bioconductor version: Release (3.18)

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))


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:

SAFE manual PDF R Script
Reference Manual PDF


biocViews DifferentialExpression, GeneSetEnrichment, Pathways, Software, StatisticalMethod
Version 3.42.0
In Bioconductor since BioC 1.6 (R-2.1) or earlier (> 19 years)
License GPL (>= 2)
Depends R (>= 2.4.0), AnnotationDbi, Biobase, methods, SparseM
System Requirements
See More
Suggests GO.db, PFAM.db, reactome.db, hgu133a.db, breastCancerUPP, survival, foreach, doRNG, Rgraphviz, GOstats
Linking To
Depends On Me
Imports Me EGSEA, EnrichmentBrowser
Suggests Me
Links To Me
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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package safe_3.42.0.tar.gz
Windows Binary safe_3.42.0.zip
macOS Binary (x86_64) safe_3.42.0.tgz
macOS Binary (arm64) safe_3.42.0.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