[BioC] About the state of KEGG-related packages

[Luo Weijun]

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 The KEGG.db and KEGGSOAP packages are no longer updated and any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 package that relies on them is also outdated.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 packages with updated or outdated information based on what they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,
>>
>