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, Laurent > 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-boun...@r-project.org] on behalf of Aaron Lun >> [a...@wehi.edu.au] >> Sent: Thursday, November 05, 2015 12:27 PM >> To: bioc-devel@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 >> >> _______________________________________________ >> Bioc-devel@r-project.org mailing list >> https://stat.ethz.ch/mailman/listinfo/bioc-devel >> >> >> This email message may contain legally privileged and/or confidential >> information. If you are not the intended recipient(s), or the employee or >> agent responsible for the delivery of this message to the intended >> recipient(s), you are hereby notified that any disclosure, copying, >> distribution, or use of this email message is prohibited. If you have >> received this message in error, please notify the sender immediately by >> e-mail and delete this email message from your computer. Thank you. >> _______________________________________________ >> Bioc-devel@r-project.org mailing list >> https://stat.ethz.ch/mailman/listinfo/bioc-devel >> > > _______________________________________________ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel -- Laurent Gatto | @lgatt0 http://cpu.sysbiol.cam.ac.uk/ http://lgatto.github.io/ _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
