To install this package, start R and enter:

source("http://bioconductor.org/biocLite.R")
biocLite("safe")

In most cases, you don't need to download the package archive at all.

safe

 

Significance Analysis of Function and Expression

Bioconductor version: Release (3.1)

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 jimmy.harvard.edu>

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

Installation

To install this package, start R and enter:

source("http://bioconductor.org/biocLite.R")
biocLite("safe")

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 3.8.0
In Bioconductor since BioC 1.6 (R-2.1) or earlier (> 10 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
Imports Me EnrichmentBrowser
Suggests Me
Build Report  

Package Archives

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

Package Source safe_3.8.0.tar.gz
Windows Binary safe_3.8.0.zip
Mac OS X 10.6 (Snow Leopard) safe_3.8.0.tgz
Mac OS X 10.9 (Mavericks) safe_3.8.0.tgz
Subversion source (username/password: readonly)
Git source https://github.com/Bioconductor-mirror/safe/tree/release-3.1
Package Short Url http://bioconductor.org/packages/safe/
Package Downloads Report Download Stats

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