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safe

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")):

Installation

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.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("safe")
SAFE manual PDF R Script
Reference Manual PDF

Details

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
Imports
System Requirements
URL
See More
Suggests GO.db, PFAM.db, reactome.db, hgu133a.db, breastCancerUPP, survival, foreach, doRNG, Rgraphviz, GOstats
Linking To
Enhances
Depends On Me
Imports Me EGSEA, EnrichmentBrowser
Suggests Me
Links To Me
Build Report Build Report

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