[Bioperl-l] drawing chromosome ideograms

Benoit Ballester benoit at ebi.ac.uk
Tue Sep 12 12:04:00 UTC 2006


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 
snapCGH : Segmentation, normalisation and processing of aCGH data.



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

Benoit Ballester
Ensembl Team
European Bioinformatics Institute (EMBL-EBI)
Wellcome Trust Genome Campus, Hinxton
Cambridge CB10 1SD, United Kingdom

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