[Bioperl-l] drawing chromosome ideograms

Guðmundur Árni Þórisson gthorisson at gmail.com
Tue Sep 12 16:46:24 EDT 2006


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Richard, ideogram.pm is part of GBrowse. I fact, I see it here in the  
GMOD CVS repository:

http://gmod.cvs.sourceforge.net/gmod/Generic-Genome-Browser/lib/Bio/
Graphics/Glyph/

Sheldon McKay (mckays at cshl.edu, is probably on this list) at CSHL did  
some more work on this Bio::Graphics glyph after my initial  
implementation (for the HapMap installation at http://www.hapmap.org/ 
cgi-perl/gbrowse), fixed some color overflow bugs and added another  
ideogram-like glyph to GBrowse (heat map). Sheldon may be able to  
help you if you want to add some more functionality and/or create new  
similar glyphs yourself for displaying CGH data.


           Mummi, University of Leicester

On Sep 12, 2006, at 1:04 PM, Benoit Ballester wrote:

> Richard,
>
> You can also have a look at Bioconductor - Some of the packages are
> specific to CGHarrays, and they are very nice.  This is obviously of
> topic on this mailling list, but if you need to normalize, analyse,  
> plot
> CGH data, I suggest these packages :
>
> cghMCR : Find chromosome regions showing common gains/losse
> aCGH : Classes and functions for Array Comparative Genomic  
> Hybridization
> data
> snapCGH : Segmentation, normalisation and processing of aCGH data.
>
> Regards,
>
> Benoit
>
> Richard Birnie wrote:
>> Hi all,
>>
>> Are their any tools in bioperl to generate chromosome ideograms  
>> for visualising CGH data? I did find an old thread (2003) in the  
>> mailing list describing someone attempting to do this in Gbrowse  
>> and the mention of a module called ideogram.pm. I had a look at  
>> Gbrowse and I'm not sure I need that level of complexity, I just  
>> need to produce a simple static PNG or JPG for reports/slides.  
>> Although if this is the only way then I'll give it a go. I  
>> couldn't find any further mention of ideogram.pm anywhere, is this  
>> part of GBrowse? I also found a mention of a glyph in  
>> Bio::Graphics for this type of thing but I can't find it again now.
>>
>> Essentially I'm looking for some pointers to what is possible in  
>> this area. If this can't be done in bioperl does anyone know of  
>> any other tools (preferably free) that can do this type of thing.
>>
>> regards,
>> Richard
>>
>> Dr Richard Birnie
>> Scientific Officer
>> Section of Pathology and Tumour Biology
>> Welcome Brenner Building, LIMM
>> St James University Hospital
>> Beckett St, Leeds, LS9 7TF
>> Tel:0113 3438624
>> e-mail: r.birnie at leeds.ac.uk
>   http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
> -- 
> Benoit Ballester
> Ensembl Team
> European Bioinformatics Institute (EMBL-EBI)
> Wellcome Trust Genome Campus, Hinxton
> Cambridge CB10 1SD, United Kingdom
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

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