[BioC] Kegg pathway --> gene network

[Sim, Fraser]

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
>
>
-- 
Cheers,
David

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