[Bioc-devel] Genomics Extension for SQLite seeking R/bioC co-maintainer

[Vincent Carey]

Thanks Mike, we're having a look.  I haven't found much comparative
benchmarking data by prowling around your site ... am I missing anything?
The colab notebook is helpful.


On Tue, Jun 1, 2021 at 5:07 AM Mike Lin <dna using mlin.net> wrote:

> Dear all,
>
> I'm writing in hopes of recruiting an R/Bioconductor co-maintainer for
> Genomics
> Extension for SQLite <https://github.com/mlin/GenomicSQLite>, which adds
> several key features to SQLite useful for bioinformatics data management;
> for example:
>
>    - streaming read/write compression layer
>    - querying compressed databases directly via web/cloud URLs
>    - Genomic Range Index for interval overlap queries
>    - in-SQL helper functions for manipulating sequences & identifiers
>
> I think this could eventually find use in many Bioconductor features, but
> as a first step, we need the essential bindings package to load the
> extension alongside RSQLite. I'm hoping somebody here might find the
> project promising enough to chip into, as I don't get to use R much in my
> own day-to-day anymore.
>
> The documentation site includes a section on writing language bindings
> <https://mlin.github.io/GenomicSQLite/bindings/> that roadmaps the
> necessary work, which I'd also be happy to work closely together on it.
> Longer term, there are many possible applications to explore, and I also
> anticipate presenting the work in suitable forums which I'd be happy to
> share in.
>
> Please contact me if interested, on this github discussion
> <https://github.com/mlin/GenomicSQLite/discussions/17>, by email
> dna using mlin.net, or this thread. Alternatively, any feedback/ideas about how
> to make the project useful are most welcome!
>
> Thanks,
> Mike Lin <https://www.mlin.net>
>
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>
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