[BioC] About the state of KEGG-related packages

[Enrico Ferrero]

Dear list,

I will soon be doing some pathway enrichment analysis and would like
to make the most of what Bioconductor has to offer, but I am a bit
confused about the current state of packages relying upon KEGG, such
as clusterProfiler, KEGGgraph, keggorthology, KEGGprofile, PathNet and
pathview, just to name a few.

As you probably know, KEGG has moved to a subscription-based model for
accessing his FTP site in 2011 [1].

The following is my understanding of how this has affected
Bioconductor, but corrections and clarifications are welcome.
The KEGG.db and KEGGSOAP packages are no longer updated and any
package that relies on them is also outdated. On the other hand, since
KEGG has continued to offer access through its REST API, the KEGGREST
package is now the preferred way to pull up to date information out of
KEGG.
On top of this, some package maintainers may have used their own
implementation to access KEGG, so there's no easy way to filter
packages with updated or outdated information based on what they
depend on.

Provided this is broadly correct, my question is: how do I know which
KEGG-related packages are reliable in terms of up-to-dateness and
which not?

Thank you.

[1] http://www.kegg.jp/kegg/download/

Best,

-- 
Enrico Ferrero
PhD Student
Steve Russell Lab - Department of Genetics
FlyChip - Cambridge Systems Biology Centre
University of Cambridge

e.ferrero at gen.cam.ac.uk
http://flypress.gen.cam.ac.uk/