[BioC] GOstats with Reactome database?
mcarlson at fhcrc.org
Mon Aug 15 23:44:15 CEST 2011
I am glad to hear that! We are definitely interested in getting
reactome better exposure through Bioconductor. We may contact you to
help facilitate this in the near future.
On 08/15/2011 02:37 PM, Robin Haw wrote:
> Dear Martin and Jose,
> We, at Reactome, would be encouraged by the development of Gostats to use
> our pathway data. If you would like to discuss this further, please let me
> Likewise, if there are any other BioConductor developers interested in
> using Reactome as a source of pathway data, drop me an email. In the
> meantime, we do provide a "Reactome Pathway Gene Set" and other annotation
> data at http://www.reactome.org/download/.
> Robin Haw, PhD
> Scientific Associate and Outreach Coordinator (Reactome)
> Ontario Institute for Cancer Research
> MaRS Centre, South Tower
> 101 College Street, Suite 800
> Toronto, Ontario, Canada M5G 0A3
> Tel: 647-260-7985
> Toll-free: 1-866-678-6427
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> On 11-08-15 1:21 PM, "J.delasHeras at ed.ac.uk"<J.delasHeras at ed.ac.uk> wrote:
>> Quoting Martin Morgan<mtmorgan at fhcrc.org> on Mon, 15 Aug 2011 10:11:50
>>> On 08/15/2011 05:48 AM, J.delasHeras at ed.ac.uk wrote:
>>>> Dear all,
>>>> with the demise of KEGG (well, at least without subscription), I was
>>>> wondering whether there are any plans to get GOstats working with the
>>>> Reactome database, or whether there is an "easy" way to persuade
>>>> to work with it.
>>> Hi Jose --
>>> Yes, we intend to revise the GOstats, GSEABase, and perhaps other
>>> packages to work more flexibly with Reactome& other data base
>>> packages. Whether this will be accomplished this release is not clear.
>>>> Any ideas?
>> Hi Martin,
>> that's great news. I have become a bit of a fan of GOstats recently
>> and would love to use a similar approach with other databases.
>> Very grateful for all your work.
>> Dr. Jose I. de las Heras Email: J.delasHeras at ed.ac.uk
>> The Wellcome Trust Centre for Cell Biology Phone: +44 (0)131 6507090
>> Institute for Cell& Molecular Biology Fax: +44 (0)131 6507360
>> Swann Building, Mayfield Road
>> University of Edinburgh
>> Edinburgh EH9 3JR
>> The University of Edinburgh is a charitable body, registered in
>> Scotland, with registration number SC005336.
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