[Bioc-devel] Why should Bioconductor developers re-use core classes?

Ryan Thompson rct at thompsonclan.org
Wed Oct 18 19:26:15 CEST 2017

I think the main reason for reusing/subclassing core classes that users can
appreciate is that it makes it much easier for users to integrate multiple
packages into a single workflow. Only the most basic of pipelines uses just
a single Bioconductor package. For instance, an "edgeR" pipeline obviously
uses the edgeR package, but it likely also uses several other packages,
like sva, RUV, variancePartition, etc. The more these different packages
operate on the same core data structures, the less work the user has to do
to use them together. And to bring that back around to an incentive for
developers, making your package interoperate with other packages more
easily means that users will be more likely to use your package.

On Tue, Oct 17, 2017 at 4:55 PM Levi Waldron <lwaldron.research at gmail.com>

> I'm putting together a presentation with a demo on why Bioconductor
> developers should re-use and extend core classes whenever possible. It
> includes a demo of some real-life consequences from two packages I use a
> lot, metagenomeSeq and phyloseq. These are far from the only examples, many
> Bioconductor packages have created new classes from scratch, and I think as
> a community we should greatly reduce that practice. I would welcome any
> feedback:
> https://www.slideshare.net/LeviWaldron/why-reuse-core-classes
> (sorry the slides are a little Frankenstein - in the interest of speed I
> made part of it in Powerpoint and part in Beamer, and used pdftk to
> concatenate these! In practice I would do the Beamer part as a live-demo,
> and take advantage of some animations in PPT)
> --
> Levi Waldron
> http://www.waldronlab.org
> Assistant Professor of Biostatistics     CUNY School of Public Health
> US: +1 646-364-9616 <(646)%20364-9616>
>        Skype:
> levi.waldron
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