safe

Significance Analysis of Function and Expression

Bioconductor version: Development (3.0)

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>

To install this package, start R and enter:

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

To cite this package in a publication, start R and enter:

    citation("safe")

Documentation

PDF R Script SAFE manual
PDF   Reference Manual

Details

biocViews FunctionalAnnotation, GeneExpression, Software
Version 3.5.0
In Bioconductor since BioC 1.6 (R-2.1) or earlier
License GPL (>= 2)
Depends R (>= 2.4.0), AnnotationDbi, Biobase, methods, SparseM
Imports
Suggests GO.db, KEGG.db, PFAM.db, reactome.db, hgu133a.db, breastCancerUPP, survival, foreach, doRNG, Rgraphviz, GOstats
System Requirements
URL
Depends On Me
Imports Me
Suggests Me

Package Downloads

Package Source safe_3.5.0.tar.gz
Windows Binary safe_3.5.0.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard) safe_3.5.0.tgz
Mac OS X 10.9 (Mavericks)
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