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

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!