[BioC] Which resources for pathway analysis?

[January Weiner]

Dear all,

my tool of choice currently is SPIA, a package that seems to provide
sophisticated analysis of pathways (including both, gene set
enrichment analysis and pathway perturbation analysis). I wonder what
other tools you could recommend? The task at hand is to identify
differentially regulated pathways given information on differentially
expressed genes, using a solid, but broad pathway database.

There is, of course, a wide range of tools outside of R (e.g.
PathVisio) which can be used for data mining and visualisation as well
as running specific statistical analyses. I wonder what are you using
in R.

kind regards,

j.

-- 
-------- Dr. January Weiner 3 --------------------------------------
Max Planck Institute for Infection Biology
Charitéplatz 1
D-10117 Berlin, Germany
Web   : www.mpiib-berlin.mpg.de
Tel     : +49-30-28460514