[BioC] Kegg pathway --> gene network
Fraser_Sim at URMC.Rochester.edu
Sat Dec 27 17:42:22 CET 2008
I am still unable to install KEGGgraph using biocLite.
Running biocinstall version 2.3.9 with R version 2.8.0
Your version of R requires version 2.3 of Bioconductor.
package 'KEGGgraph' is not available
R version 2.8.0 (2008-10-20)
attached base packages:
 stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
Any idea when this package might be ready?
From: bioconductor-bounces at stat.math.ethz.ch
[mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Jitao David
Sent: Friday, December 12, 2008 6:29 AM
To: bioconductor at stat.math.ethz.ch
Subject: Re: [BioC] Kegg pathway --> gene network
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
I am the maintainer of this package and am ready to answer your
> 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
> help the community to construct an equivalent gene network from
> pathway database like KEGG.
> For e.g. To find all genes available in Glycolysis pathway and
> the direction of arcs between metabolites, to construct an equivalent
> regulatory network from the same.
> off course doing this manually and construct a graphNel object is
> but to do this for more pathways would be cumbersome, so was wondering
> there are any tools available in this regard or any pointers .?
> Any information would be of great help.
> Thanks in advance,
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