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

Mike Lin dn@ @end|ng |rom m||n@net
Tue Jun 1 11:07:04 CEST 2021

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!

Mike Lin <https://www.mlin.net>

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