Okay, some meat and bones are on GitHub now:
https://github.com/LTLA/InteractionSet
The idea is to represent genomic interactions as pairs of genomic
regions, using indices to point to a common GRanges object (a la Hits,
though I haven't used that explicitly due to the presence of additional
It also seems worth mentioning that the graph package (
http://bioconductor.org/packages/release/bioc/html/graph.html)
has reasonable numbers of dependers and importers and could
undoubtedly play a role in feature-feature management.
On Sun, Nov 8, 2015 at 8:49 AM, Vincent Carey
wrote:
> In our
In our discussions of the multiassay object/analysis problem,
https://github.com/vjcitn/biocMultiAssay
Kasper Hansen has suggested elaborations of the Hits API (see for example
sec. 4 of
http://bioconductor.org/packages/release/bioc/vignettes/GenomicRanges/inst/doc/GenomicRangesIntroduction.pdf
Thanks for the interest, everyone. I'll try to put up what I've
currently got onto my GitHub page, sometime over the week.
Currently, I'm calling it an "InteractionSet" object; it builds off the
SummarizedExperiment0 class and adds some stuff to handle pairwise
genomic interactions.
- Aaron
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 s
