safe

DOI: 10.18129/B9.bioc.safe    

This package is for version 3.13 of Bioconductor; for the stable, up-to-date release version, see safe.

Significance Analysis of Function and Expression

Bioconductor version: 3.13

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 hms.harvard.edu>

Installation

To install this package, start R (version "4.1") and enter:

if (!requireNamespace("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")

 

PDF	R Script	SAFE manual
PDF		Reference Manual

Details

biocViews	DifferentialExpression, GeneSetEnrichment, Pathways, Software, StatisticalMethod
Version	3.32.0
In Bioconductor since	BioC 1.6 (R-2.1) or earlier (> 16.5 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	PCGSE
Imports Me	EGSEA, EnrichmentBrowser
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	safe_3.32.0.tar.gz
Windows Binary	safe_3.32.0.zip
macOS 10.13 (High Sierra)	safe_3.32.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/safe
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/safe
Package Short Url	https://bioconductor.org/packages/safe/
Package Downloads Report	Download Stats