Quantitative Pathway Analysis

[David]

Hi All,

I asked Doug to create this thread for those of us who are interested in quantitative systems biology, rather than the typically employed "qualitative" version which gets published (pretty pictures, a few GO term assignments, etc). Over the coming days, the hope is that several of the important players in this field will contribute their ideas and links to their software solutions. Currently, several of us are participating in the fourth PathProt Conference (http://gtpb.igc.gulbenkian.pt/PathProt/), including representatives from GeneXplain, EBI (Reactome), the Max Planck Institute for Molecular Genetics, etc. The hope is that this will provide a forum for these creators of software solutions to get feedback on what the real users think and will therefore provide a platform for them to implement said changes.


Thanks,

David

[woa]

Anybody used the MMG R package?

http://cran.r-project.org/web/packages/MMG/vignettes/MMG.pdf

[woa]

I've come across this R package some time ago:

http://cran.r-project.org/web/packages/RHT/RHT.pdf

The corresponding paper is available here:
http://pubs.amstat.org/doi/pdfplus/10.1198/jasa.2011.ap10599
Supp. Info.:
http://pubs.amstat.org/doi/suppl/10.1198/jasa.2011.ap10599