[BioC] About the state of KEGG-related packages

[Enrico Ferrero]

Dear Calin and Weijun,

Thanks for your suggestions, I will look at both packages.

Best,

On 30 July 2013 02:42, Luo Weijun <luo_weijun at yahoo.com> wrote:
> Hi Enrico,
> Pathview downloads the latest KEGG pathway data in real time following REST-like URL mechanism. It was written for pathway analysis and data visualization/integration. Should fits your needs well.
>
> The package is available at: http://bioconductor.org/packages/release/bioc/html/pathview.html
> It was published recently at: http://bioinformatics.oxfordjournals.org/content/29/14/1830.full
> The package vignette describes workflows/exmaples on microarray data (gene data) and metabolomics data (compound data), although it works for arbitrary others data types mappable to pathways.
> I also described a Pathview+GAGE workflow on RNA-seq data pathway analysis at: https://stat.ethz.ch/pipermail/bioconductor/2013-July/054021.html
> HTH.
> Weijun
>
>
> On 29 July 2013 19:37, Marc Carlson <mcarlson at fhcrc.org> wrote:
>> Hi Enrico,
>>
>> In general, I think you should assume that almost all KEGG resources are out
>> of date since KEGG basically cut the world off with a pay wall some time
>> ago.
>>
>> The only exception I know of with any certainty is KEGGREST.  And that is
>> only because KEGG has (at least for now) decided to allow continued access
>> to their REST API.
>>
>>
>>   Marc
>>
>>
>>
>>
>>
>> On 07/28/2013 02:42 PM, Enrico Ferrero wrote:
>>>
>>> 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 The KEGG.db and KEGGSOAP packages are no longer updated and any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 package that relies on them is also outdated.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/