Bayesian networks in BioC
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@jacob-michaelson-1079
Last seen 7.1 years ago
Hi all, I looked around on the BioC site for information on any implementations of Bayesian networks in Bioconductor. I couldn't find anything. From the literature it looks like Bayesian networks for gene expression has been around for almost as long as microarrays, yet no implementations exist in R/Bioconductor - which seemed a little odd to me. Is there a reason for this? Are Bayesian networks somehow dubious, or is it just that nobody has written a package? Would love to hear from the experts... Thanks, Jake
Bayesian Bayesian • 811 views
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@henrik-bengtsson-4333
Last seen 4 months ago
United States
Another word for Bayesian networks is graphical models. On Bioconductor, "GraphsAndNetworks" on http://www.bioconductor.org/packages/release/Software.html is probably a good start. I believe geneTS is one such package. On CRAN, a great page for this is http://cran.r-project.org/src/contrib/Views/gR.html. Hope this helps Henrik On 5/26/06, Jacob Michaelson <jjmichael at="" comcast.net=""> wrote: > Hi all, > > I looked around on the BioC site for information on any > implementations of Bayesian networks in Bioconductor. I couldn't > find anything. From the literature it looks like Bayesian networks > for gene expression has been around for almost as long as > microarrays, yet no implementations exist in R/Bioconductor - which > seemed a little odd to me. Is there a reason for this? Are Bayesian > networks somehow dubious, or is it just that nobody has written a > package? > > Would love to hear from the experts... > > Thanks, > > Jake > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > >
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alex lam RI ▴ 310
@alex-lam-ri-1491
Last seen 7.1 years ago
hi Jacob, Sorry, I am not an expert and in fact just a newbie in statistical genetics and R. There is a package called "deal" in CRAN for Bayesian Network Learning. Never used it before though. Cheers, Alex Alex C. Lam PhD student Dept. of Genetics and Genomics Roslin Institute, Edinburgh EH25 9PS UK -----Original Message----- From: bioconductor-bounces@stat.math.ethz.ch on behalf of Jacob Michaelson Sent: Sat 5/27/2006 12:27 AM To: Bioconductor Subject: [BioC] Bayesian networks in BioC Hi all, I looked around on the BioC site for information on any implementations of Bayesian networks in Bioconductor. I couldn't find anything. From the literature it looks like Bayesian networks for gene expression has been around for almost as long as microarrays, yet no implementations exist in R/Bioconductor - which seemed a little odd to me. Is there a reason for this? Are Bayesian networks somehow dubious, or is it just that nobody has written a package? Would love to hear from the experts... Thanks, Jake _______________________________________________ Bioconductor mailing list Bioconductor at stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
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On May 27, 2006, at 8:08 AM, alex lam ((RI)) wrote: > > There is a package called "deal" in CRAN for Bayesian Network > Learning. Never used it before though. > > Cheers, > Alex On May 27, 2006, at 10:09 AM, Henrik Bengtsson wrote: > Another word for Bayesian networks is graphical models. > > On Bioconductor, "GraphsAndNetworks" on > http://www.bioconductor.org/packages/release/Software.html is probably > a good start. I believe geneTS is one such package. > > On CRAN, a great page for this is > http://cran.r-project.org/src/contrib/Views/gR.html. > > Hope this helps > > Henrik Thanks for the tips. This will give me a great start. I'm not a statistician, either, so I didn't know all the Bayesian networks synonyms to help in my search. I've just read a little more about them and they seem to be painted as some sort of "silver bullet" (compared to traditional clustering techniques) for teasing out relationships among genes. I wanted to give them a shot, but couldn't find the right packages - until now. Thanks guys, Jake
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