[Bioc-devel] Extending biovizBase and ggbio packages

Morgan, Martin Martin.Morgan at roswellpark.org
Mon Dec 14 15:44:06 CET 2015

The mirror doesn't accept pull requests (the repository owner would have to handle the pull request, and package maintainers are not the owners of the mirror; this will eventually change). Provide a diff against the mirror, and patch in svn, or package maintainer fork the mirror (http://bioconductor.org/developers/how-to/git-mirrors/) and pull against that.
From: Bioc-devel [bioc-devel-bounces at r-project.org] on behalf of Michael Lawrence [lawrence.michael at gene.com]
Sent: Monday, December 14, 2015 8:46 AM
To: Rainer Johannes
Cc: Luo Weijun via Bioc-devel
Subject: Re: [Bioc-devel] Extending biovizBase and ggbio packages

Sounds very useful. Perhaps you could make a github pull request on
the Bioconductor mirrors of those packages. Then Tengfei or I could
look it over.

Btw, I like the filtering functionality in ensemldb. Would be nice to
have something as rich for TxDb. Would be great if there were
convenience wrappers like subset() and sort(). Like
transcripts(sort(subset(db, seqname == "chr1"), by = geneSymbol)).


On Mon, Dec 14, 2015 at 4:12 AM, Rainer Johannes
<Johannes.Rainer at eurac.edu> wrote:
> Dear all,
> I’ve modified the biovizBase and ggbio packages so that they do directly support EnsDb annotations (just like annotations provided by TxDb objects/packages).
> Is there a way I could provide these changes? I’ve directly contacted Tengfei last week, but did not get any reply yet…
> cheers, jo
> _______________________________________________
> Bioc-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel

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