DOI: 10.18129/    

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

Significance Analysis of Function and Expression

Bioconductor version: Development (3.9)

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>

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


To install this package, start R (version "3.6") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
BiocManager::install("safe", version = "3.9")

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:



PDF R Script SAFE manual
PDF   Reference Manual


biocViews DifferentialExpression, GeneSetEnrichment, Pathways, Software, StatisticalMethod
Version 3.23.0
In Bioconductor since BioC 1.6 (R-2.1) or earlier (> 14 years)
License GPL (>= 2)
Depends R (>= 2.4.0), AnnotationDbi, Biobase, methods, SparseM
Suggests GO.db, PFAM.db, reactome.db, hgu133a.db, breastCancerUPP, survival, foreach, doRNG, Rgraphviz, GOstats
Depends On Me
Imports Me EGSEA, EnrichmentBrowser
Suggests Me
Links To Me
Build Report  

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

Source Package safe_3.23.0.tar.gz
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Mac OS X 10.11 (El Capitan) safe_3.23.0.tgz
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