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 at 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 at 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> [[alternative HTML version deleted]]
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