[Biopython-dev] GEO Libraries

[Peter Cock]

On Tue, Dec 6, 2011 at 12:29 AM, Morgan Maddren <mmaddren at soe.ucsc.edu> wrote:
> Hi, I don't know who this may concern, but I noticed on the wiki
> that there is interest in GEO SOFT parsers/writers. I work for
> the UCSC Genome Browser, and we've already created libraries
> for working with SOFT files, and would be happy to share.
>
> -Morgan

In Python? ;)

We have an old and somewhat rudimentary set of GEO SOFT
parsers under Bio.Geo, see:
https://github.com/biopython/biopython/tree/master/Bio/Geo

But not much else. Here R/Bioconductor is much more mature,
not just Sean Davis' GEO parser but the whole microarray
expression set objects, plus of course the statistics side (for
which we may want to use SciPy).

Peter