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Eddie Ruiz

@ed2uiz.bsky.social

https://ed2.dev/

17 Posts59 Follower674 Folgt
SMT@pp0196.bsky.social · 4w ago

This is great work, happy to see DuckDB usage in this space. Related self plug, i made a HTS file formats reader extension rgenomicsetl.r-universe.dev/Rduckhts that allow fast imports directly into duckb and avoid RSamtools and al. There are community readers for single cell formats

Rduckhts: 'DuckDB' High Throughput Sequencing File Formats Reader Extension

Bundles the 'duckhts' 'DuckDB' extension for reading High Throughput Sequencing file formats with 'DuckDB'. The 'DuckDB' C extension API <https://duckdb.org/docs/stable/clients/c/api> and its 'htslib'...

rgenomicsetl.r-universe.dev

Eddie Ruiz@ed2uiz.bsky.social · 4w ago

Can databases scale scientific analyses beyond RAM? I’m excited to share dbverse, a composable database framework built to do just that. Across benchmarks, dbverse delivers ~1000x speedups and scales #spatialomics analyses to millions of cells. Preprint: www.biorxiv.org/content/10.6... 1/🧵

dbverse scales spatial omics analysis with embedded analytical databases

Spatial omics datasets are increasing in size and complexity, exceeding the memory of standard computers and thereby limiting data analysis. Here we present dbverse, a framework for larger-than memory...

biorxiv.org