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This is the development version of safe; for the stable release version, see safe.

Significance Analysis of Function and Expression

Bioconductor version: Development (3.20)

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>

Citation (from within R, enter citation("safe")):


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))

# The following initializes usage of Bioc devel


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 3.45.0
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 ReporterScore
Links To Me
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Package Archives

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

Source Package safe_3.45.0.tar.gz
Windows Binary
macOS Binary (x86_64) safe_3.45.0.tgz
macOS Binary (arm64) safe_3.45.0.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
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