Significance Analysis of Function and Expression
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.
R (>= 2.4.0), AnnotationDbi, Biobase, methods, SparseM
GO.db, PFAM.db, reactome.db, hgu133a.db, breastCancerUPP,
survival, foreach, doRNG, Rgraphviz, GOstats
DifferentialExpression, Pathways, GeneSetEnrichment,
StatisticalMethod, Software