[BioC] pack (mainly) for E.coli genome (and possibly other circular genomic entities)

[Laurent Gautier]

Hi,


I crafted together few functions and data I had for the analysis
of E. coli data on project. This is sort of Affymetrix GeneChip type
'ecoligenome' oriented, but I believe the pack has functions
generic enough to deal with other Eukaryots, mostly on the
plotting side of things (the 'circle' representation has been around
for quite some time among the microbiologits community, see
http://genolist.pasteur.fr/Colibri/ ,
http://www.cbs.dtu.dk/staff/dave/MScourse/GenomeAtlas_intro.html).
There is also a little to perform 'sliding window operations' on
strings (a la 'cumulative G-C skew' once so hype, see:
http://nar.oupjournals.org/cgi/content/abstract/26/10/2286?ijkey=1656931395e28454c697cd6b629a325792356b35&keytype2=tf_ipsecsha).  
.

The functions are most likely to go into the pack 'geneplotter'
as soon as possible and the data are thought to end in a data package
(next release I would think. the functions are mostly ok but 
more data are definitely needed). Having them together to play is
the best thing I could figure out get polished before throwing them in.

The package is called 'ecolitk' (for ecoli tool kit) and can be found 
in the CVS page of the bioconductor website. 
For those who carefully keep away from CVS, 
I put together a simple download page:
http://www.cbs.dtu.dk/laurent/download/ecolitk

Feedback is fairly welcome.



L.



-- 
--------------------------------------------------------------
currently unspecified location 
--------------------------------------------------------------
Laurent Gautier			CBS, Building 208, DTU
PhD. Student			DK-2800 Lyngby,Denmark	
tel: +45 45 25 24 89		http://www.cbs.dtu.dk/laurent