> If not, the general consensus seemed to be that Pathway Commons and > reactome.db etc. were the way forward Is there a way to directly access the Pathway Commons data from R? For example, to do enrichment analysis? Reactome.db has its own package, I think. j. > > I too am sad that KEGG could not be funded in the public interest but I > guess that is the fallout from a recession. > > > On Mon, Jan 16, 2012 at 12:58 AM, Asta Laiho <asta.laiho at="" btk.fi=""> wrote: > >> Hi, >> >> I just saw the following information regarding the continuation of the >> KEGG.db Bioconductor package: >> >> KEGG.db contains mappings based on older data because the original >> ?resource was removed from the the public domain before the most >> ?recent update was produced. This package should now be considered >> ?deprecated and future versions of Bioconductor may not have it >> ?available. ?One possible alternative to consider is to look at the >> ?reactome.db package >> >> I am very sad to hear about the news as KEGG has become an important >> resource for the researchers and using it through Bioconductor has been >> very valuable for many people. I'm not sure what the original reason for >> removing the database content form the public domain is, officially I found >> the following information: >> >> Plea to support KEGG >> http://www.kegg.jp/kegg/docs/plea.html >> and the comment in the Editorial of the NAR DB issue >> (Nucl. Acids Res. 2012 40 D1: D1-D8). >> http://nar.oxfordjournals.org/content/40/D1/D1.full >> >> If someone has further information for clarifying the situation it would >> be great to share it on the emailing list. >> >> - Asta >> >> >> ? ? ? ?[[alternative HTML version deleted]] >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> > > > > -- > If people do not believe that mathematics is simple, > it is only because they do not realize how complicated life is. John von > Neumann<http: www-groups.dcs.st-="" and.ac.uk="" ~history="" biographies="" von_neumann.html=""> > > ? ? ? ?[[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- -------- Dr. January Weiner 3 -------------------------------------- Max Planck Institute for Infection Biology Charit?platz 1 D-10117 Berlin, Germany Web?? : www.mpiib-berlin.mpg.de Tel? ?? : +49-30-28460514