Question: Are bioconductor packages designed for enrichment analysis affected by KEGG privatization ?
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gravatar for Radhouane Aniba
8.4 years ago by
Radhouane Aniba240 wrote:
Hi, Some bioconductor packages like GSEA or GOStats that additionally to GO are designed to measure gene set enrichment using KEGG pathways, still work and give results even after the new paid license and subscription like we all know the story. My question can be discussed in two different ways, I am wondering how people developing these packages are doing ? Does thes packages call KEGG directly or an image of it, if this is the second case how a user can be sure about the KEGG version used ? The second part of my question concerns the development of other packages for gene set enrichment, do you expect this kind of packages decreasing in the coming few years due to KEGG privatization ? if now, how can we ( for late people like me) download an image of KEGG database corresponding to a version existing before privatization, as it was in public domain it is not going against the new license rules to distribute it. Regards Radhouane -- *Radhouane Aniba* *Bioinformatics Postdoctoral Research Scientist* *Institute for Advanced Computer Studies Center for Bioinformatics and Computational Biology* *(CBCB)* *University of Maryland, College Park MD 20742* [[alternative HTML version deleted]]
pathways gostats • 537 views
ADD COMMENTlink modified 8.4 years ago by Marc Carlson7.2k • written 8.4 years ago by Radhouane Aniba240
Answer: Are bioconductor packages designed for enrichment analysis affected by KEGG priv
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gravatar for Marc Carlson
8.4 years ago by
Marc Carlson7.2k
United States
Marc Carlson7.2k wrote:
Hi Radhouane, The loss of KEGG is a real bummer for the community, but there are other resources on the horizon and some that are already available. You can for example check out the reactome.db package (contributed by Willem Ligtenberg) and note that it has a lot of the same kinds of information as the KEGG.db package has traditionally had. And software packages like GOstats can just be enhanced to work with new resources as they come online, and in the meantime they will still work with older packages based on the older snapshots from when KEGG was still freely available. So in short, life goes on. With or without KEGG, there will continue to be many great ways to do pathway analysis for the simple reason that there is still a community of bright people like yourself who are interested in those questions. Marc On 08/03/2011 10:42 AM, Radhouane Aniba wrote: > Hi, > > Some bioconductor packages like GSEA or GOStats that additionally to GO are > designed to measure gene set enrichment using KEGG pathways, still work and > give results even after the new paid license and subscription like we all > know the story. > > My question can be discussed in two different ways, I am wondering how > people developing these packages are doing ? Does thes packages call KEGG > directly or an image of it, if this is the second case how a user can be > sure about the KEGG version used ? > > The second part of my question concerns the development of other packages > for gene set enrichment, do you expect this kind of packages decreasing in > the coming few years due to KEGG privatization ? if now, how can we ( for > late people like me) download an image of KEGG database corresponding to a > version existing before privatization, as it was in public domain it is not > going against the new license rules to distribute it. > > Regards > > Radhouane > >
ADD COMMENTlink written 8.4 years ago by Marc Carlson7.2k
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