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

Levi Waldron lwaldron.research at gmail.com
Fri Mar 9 13:15:16 CET 2018

On Thu, Mar 8, 2018 at 12:29 AM, Paul Shannon <pshannon at systemsbiology.org>

> Thanks, Gabe.
> You make an excellent point: bioc objects get first class support.  In
> some instance, base R data types deserve that also, and data.frames lead
> the list for me, being useful, concise, universally available, expressive.
> So perhaps not “data.frames replaced by” but “accompanied by” appropriate
> bioc data types?
>  - Paul

Definitely +1 for supporting GenomicRanges, including what's in genome()
and mcols(). There's a demo of an rtracklayer -> GRanges -> UCSC genome
browser workflow in the rtracklayer vignette
I've made use of. I wouldn't necessarily say *don't* support data.frame,
but I would certainly encourage Bioc users to import data with rtracklayer
instead of generic read* functions, and to take advantage of the vast
AnnotationHub and OrganismDbi-based annotations which provide GenomicRanges

Thanks and looking forward to it!

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