Question: GOstats-compatible annotation package for Helicobacter pylori 26995
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gravatar for Klaus-Peter Pleissner
10.9 years ago by
Klaus-Peter Pleissner70 wrote:
Hi BioC, in the BioC-mailing list I have read a lot about annotation packages for GOstats or topGO. My question is following: 1. Is there already a user-defined GOstats-compatible annotation package for Helicobacter pylori 26995 to perform gene enrichment analysis using , for instance, hyperGtest ? 2. Which package should I use ? GOstats or topGO or are there others, too ? 3. How to create such new annotation package ? AnnBuilder or other R-packages ? BTW, for human genes we are using WebGestalt (http://bioinfo.vanderbilt.edu/webgestalt/) to perform gene enrichment analysis, but WebGestalt doesn't run for bacterial gene lists. Thanks for hints or advices! Klaus-Peter -- Mit freundlichen Gr?ssen / Best regards Dr. Klaus-Peter Pleissner Max Planck Institute for Infection Biology Core Facility Bioinformatics Charit?platz 1 D-10117 Berlin Germany *Phone:* +49-30-28460-119 *Fax:* +49-30-28460-507 *URL:* http://web.mpiib-berlin.mpg.de/bioinformatik <http: web="" .mpiib-berlin.mpg.de="" bioinformatik=""/> *Email:* pleissner at mpiib-berlin.mpg.de <mailto:pleissner at="" mpiib-="" berlin.mpg.de="">
ADD COMMENTlink modified 10.9 years ago by Marc Carlson7.2k • written 10.9 years ago by Klaus-Peter Pleissner70
Answer: GOstats-compatible annotation package for Helicobacter pylori 26995
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gravatar for Marc Carlson
10.9 years ago by
Marc Carlson7.2k
United States
Marc Carlson7.2k wrote:
Hi Klaus-Peter, The normal way to make annotation packages is to use the SQLForge functions in the AnnotationDbi package. But before you can do that we have to support that organism with some code to maintain an intermediate database. I wish I could tell you that we support H. pylori but we don't yet. Currently the only microrganisms we support are E. coli, yeast and the malaria parasite. Perhaps you could help me add H. pylori to the list of supported organisms? Please email me about this so we can work on a solution together. Marc Klaus-Peter Pleissner wrote: > Hi BioC, > > in the BioC-mailing list I have read a lot about annotation packages > for GOstats or topGO. My question is following: > 1. Is there already a user-defined GOstats-compatible annotation > package for Helicobacter pylori 26995 to perform gene enrichment > analysis using , for instance, hyperGtest ? > 2. Which package should I use ? GOstats or topGO or are there others, > too ? > 3. How to create such new annotation package ? AnnBuilder or other > R-packages ? > > BTW, for human genes we are using WebGestalt > (http://bioinfo.vanderbilt.edu/webgestalt/) to perform gene > enrichment analysis, but WebGestalt doesn't run for bacterial gene lists. > > Thanks for hints or advices! > Klaus-Peter
ADD COMMENTlink written 10.9 years ago by Marc Carlson7.2k
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