safe

DOI: 10.18129/B9.bioc.safe    

This package is for version 3.14 of Bioconductor; for the stable, up-to-date release version, see safe.

Significance Analysis of Function and Expression

Bioconductor version: 3.14

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>

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

Installation

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

 

PDF R Script SAFE manual
PDF   Reference Manual

Details

biocViews DifferentialExpression, GeneSetEnrichment, Pathways, Software, StatisticalMethod
Version 3.34.0
In Bioconductor since BioC 1.6 (R-2.1) or earlier (> 17 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_3.34.0.tar.gz
Windows Binary safe_3.34.0.zip
macOS 10.13 (High Sierra) safe_3.34.0.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

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