[BioC] pathway analysis package

[Robert Gentleman]

There is a KEGG package, and we also have KEGGSOAP that give you access  
to the KEGG data (for non-commercial use, if I recall correctly). You  
can supplement this with the graph package, RBGL and Rgraphviz to do  
most of the pathway stuff you want to.

  Another option is to make use of the CMAP data, which is potentially  
more interesting because it has the pathways already represented as a  
graph. But it is also more work as we have not managed to build any  
interfaces for this (they have some though);
   the url is http://cmap.nci.nih.gov/PW

  Robert

On Dec 16, 2004, at 3:11 PM, Josephine Liang wrote:

> Hi, fellow bioconductor members;
>
> In my memory, there is a vague rememberance that this is a package in  
> Bioconductor called Pathway, I went to Bioconductor site , could not  
> find a package named pathway in release 1.5, did I remember it wrong?  
> Or the package is in an older release?  If it is, which release it is?  
>  how do I access it?
>
> Thanks for all your help in advance
>
> Josephine
>
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>
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| Robert Gentleman              phone: (206) 667-7700                    
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| Head, Program in Computational Biology   fax:  (206) 667-1319   |
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