[BioC] Kegg pathway --> gene network

[Martin Morgan]

Hi Fraser -- New packages are added to the 'devel' branch of 
Biocondcutor. 'devel' packages require the 'devel' version of R. You're 
using the 'release' version of R.

http://cran.fhcrc.org/bin/windows/base/rdevel.html

Martin

Sim, Fraser wrote:
> Hi David-
> 
> I am still unable to install KEGGgraph using biocLite.
> 
>> source("http://www.bioconductor.org/biocLite.R")
>> biocLite("KEGGgraph")
> Running biocinstall version 2.3.9 with R version 2.8.0 
> Your version of R requires version 2.3 of Bioconductor.
> Warning message:
> package 'KEGGgraph' is not available 
>> sessionInfo()
> R version 2.8.0 (2008-10-20) 
> i386-pc-mingw32 
> 
> locale:
> LC_COLLATE=English_United States.1252;LC_CTYPE=English_United
> States.1252;LC_MONETARY=English_United
> States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252
> 
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
> 
> 
> loaded via a namespace (and not attached):
> [1] tools_2.8.0
> 
> Any idea when this package might be ready?
> 
> Cheers,
> Fraser
> 
> -----Original Message-----
> From: bioconductor-bounces at stat.math.ethz.ch
> [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Jitao David
> Zhang
> Sent: Friday, December 12, 2008 6:29 AM
> To: bioconductor at stat.math.ethz.ch
> Subject: Re: [BioC] Kegg pathway --> gene network
> 
> Hi Anand,
> 
>   The package 'KEGGgraph' does exactly the task you need. It is added to
> bioc-devel these days and I assume it will be available from bioc-devel
> before holidays.
> 
>   I am the maintainer of this package and am ready to answer your
> questions
> around it.
> 
> Best wishes,
> David
> 
>> Hi Everyone,
>>
>> I had been searching over google but to no avail. Actually I had been
>> searching on the net for any equivalent package in bioconductor which
> would
>> help the community to construct an equivalent gene network from
> available
>> pathway database like KEGG.
>>
>> For e.g. To find all genes available in Glycolysis pathway and
> depending on
>> the direction of arcs between metabolites, to construct an equivalent
> gene
>> regulatory network from the same.
>>
>>
>>
>> off course doing this manually and construct a graphNel object is
> possible,
>> but to do this for more pathways would be cumbersome, so was wondering
> if
>> there are any tools available in this regard or any pointers  .?
>>
>>
>>
>> Any information would be of great help.
>>
>>
>>
>> Thanks in advance,
>>
>> Anand
>>
>>