[BioC] visualizing genomic data

Marc Carlson mcarlson at fhcrc.org
Fri Nov 11 02:31:36 CET 2011

Hi Bogdan,

You might also want to take a look at the new r3Cseq package.


On 11/09/2011 10:14 PM, Tengfei Yin wrote:
> Hi Bogdan,
> You could try package GenomeGraph which pull data from Biomart to create
> annotation tracks inside R.
> If you are familiar with core Bioc object like GRanges/TranscriptDb, you
> can try package ggio, you need to construct your data as GRanges and bundle
> them by tracks() function. or grid.arrange() in gridExtra package. ggbio is
> a new package, let me know if you come across any problem or you want to
> request a new feature.
> Or you can fire your data into UCSC genome browser inside R, check
> browserGenome function in package rtracklayer.
> Interaction between locus is tricky, I don't know about other packages(if
> there is any, please let me know, thanks), it could be represented as links
> in circular view,  or links in a grand linear view, which is currently
> still under development in ggbio and visnab, I will keep you post it, if
> you would like to test some functionality.
> cheers
> Tengfei
> On Wed, Nov 9, 2011 at 11:30 PM, Bogdan Tanasa<tanasa at gmail.com>  wrote:
>> Dear all,
>> I would appreciate if you can recommend any BioC package where I can
>> display togheter a set of features/annotations (eg genes, TF binding
>> sites), and 3C interactions data (the 3C chromosomal interactions will be
>> represented as lines between interaction loci, or just simply as dots that
>> count for an interaction strength at a particular position). thanks,
>> bogdan
>>         [[alternative HTML version deleted]]
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