[Bioc-devel] IGV - a new package in preparation

Gabe Becker becker.gabe at gene.com
Wed Mar 7 23:40:24 CET 2018


Sounds cool! My one note after a quick first pass is that here:

On Wed, Mar 7, 2018 at 2:15 PM, Paul Shannon <pshannon at systemsbiology.org>
> Note that though igv.js typically gets its track data from CORS/indexed
> webservers, the IGV package will also support locally created R data.frames
> describing either bed or wig tracks - annotation and quantitative,
> respectively - without any need to host those tracks on a pre-existing
> webserver.  httpuv includes a minimal webserver which can adequately serve
> the temporary files IGV creates from your data.frames.

It seems to me that those data.frames should be replaced with the core
Bioconductor object classes which represent the types of information being
displayed.  You might look to epivizr for  inspiration here, which (IIRC)
allows "tracks" within epiviz to be backed by bioconductor objects.


>  - Paul
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> Bioc-devel at r-project.org mailing list
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Gabriel Becker, Ph.D
Bioinformatics and Computational Biology
Genentech Research

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