[Bioc-devel] Base class for interaction data - expressions of interest

Laurent Gatto lg390 at cam.ac.uk
Sun Nov 8 14:05:38 CET 2015

On  7 November 2015 19:58, Ludwig Geistlinger wrote:

> I agree with Martin, I would love to see something like that.
> Especially if this would not be restricted to chromatin interactions, but
> also allows to represent protein-protein, transcriptionFactor-targetGene,
> miRNA-mRNA etc (e.g. via suitably tailored subclasses).

I would be delighted to help out in PPI (or Protein-anything
interactions) infrastructure development, if this is in scope.

Best wishes,


> This might nicely work together with bringing in existing regulatory
> networks via AnnotationHub ...
> If help is needed, I'm happy to contribute ...
> Best,
> Ludwig
>> Just to say that this is a great idea. If this starts as a github package
>> (or in svn, we can create a location for you if you'd like) I and others
>> would I am sure be happy to try to provide any guidance / insight. The
>> main design principles are probably to reuse as much as possible from
>> existing classes, especially the S4Vectors / GRanges world, and to
>> integrate metadata as appropriate (like SummarizedExepriment, for
>> instance).
>> Martin
>> ________________________________________
>> From: Bioc-devel [bioc-devel-bounces at r-project.org] on behalf of Aaron Lun
>> [alun at wehi.edu.au]
>> Sent: Thursday, November 05, 2015 12:27 PM
>> To: bioc-devel at r-project.org
>> Subject: Re: [Bioc-devel] Base class for interaction data - expressions of
>>      interest
>> There's a growing number of Bioconductor packages dealing with
>> interaction data; diffHic, GenomicInteractions, HiTC, to name a few (and
>> probably more in the future). Each of these packages defines its own
>> class to store interaction data - DIList for diffHic,
>> GenomicInteractions for GenomicInteractions, and HTClist for HiTC.
>> These classes seem to share a lot of features, which suggests that they
>> can be (easily?) replaced with a common class. This would have two
>> advantages - one, developers of new and existing packages don't have to
>> continually write and maintain new classes; and two, it provides users
>> with a consistent user experience across the relevant packages.
>> My question is, does anybody have anything in the pipeline with respect
>> to a base package for an interaction class? If not, I'm planning to put
>> something together for the next BioC release. To this end, I'd welcome
>> any ideas/input/code; the aim is to make a drop-in replacement (insofar
>> as that's possible) for the existing classes in each package.
>> Cheers,
>> Aaron
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Laurent Gatto | @lgatt0

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