The original R package for SAFE (version 1.0) is available on Bioconductor
Go to Bioconductor
and follow the links to Release Packages for this version of SAFE.
SAFE version 2.0 incorporates features from Barry et al. 2007 and several new functions to
enhance the presentation and plotting of results.
A fully documented package for Bioconductor is still under development, but the
source code, example of usage,
and a partial vignette are available. Please
contact Bill Barry with questions or comments.
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Barry WT, Nobel AB, Wright FA. (2005)
Significance analysis of functional categories in gene expression studies:
a structured permutation approach.
Bioinformatics 21(9):1943-9.
Supplementary Table Supplementary Figure 1 Supplementary Figure 2 Supplementary Figure 3 Supplementary Figure 4 Barry WT, Nobel AB, Wright FA. (2008) A statistical framework for testing functional categories in microarray data. Annals of Applied Statistics 2(1):286-315. |