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

[Levi Waldron]

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

> 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
<http://bioconductor.org/packages/release/bioc/vignettes/rtracklayer/inst/doc/rtracklayer.pdf>
that
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
objects.

Thanks and looking forward to it!

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