I published a new post, this time trying to make the most of the little RAM I had to create a #TileDB #soma - a #singlecell format and database - but for the complete #LINCS 2020 dataset. A measly 140GB+ of data.

I didn't want to re-invent the wheel, so ended converting between multiple file formats to avoid as many in-memory operations as possible.

https://amjdomingues.com/posts/2025-11-02-cmap-tile-db-build/

There are probably less evolved ways of doing this, but this is the one my technical skills allowed:)

#RStats

New blog post on #tiledb and #snowflake integration and what is possible for #biomedical #research and what I wish I could do in #duckdb

https://brianrepko.github.io/blog/posts/2025-12-20-tiledb-snowflake/

Any #tiledb #scRNA users out there?

I am ingesting data from an `h5ad` file into a soma with `tiledbsoma.io.from_h5ad` (#python API).

Does this function load the entire h5ad into memory before conversion? Python keeps crashing which I am guessing are OOO issues. If yes, is there another option to do this conversion without loading the data in memory?

It would be strange if the only option is to load the whole thing into memory considering how massive scRNA datasets are these days.

New #tiledb #soma issue created:

R-api: no support for DelayedMatrix when writing a soma from SingleCellExperiment

https://github.com/single-cell-data/TileDB-SOMA/issues/4291

Full Stack Sofware Engineer

UCLouvain

For the UCLouvain's e-OMIX project, we are hiring Full Stack Software Engineer to build and deploy an omics data exchange platform.

See the full job description on jobRxiv: https://jobrxiv.org/job/uclouvain-27778-full-stack-sofware-engineer/?feed_id=77181

#data_science #FHIR #multi_omics #omics #rest_api #tiledb #ScienceJobs #hiring #research
https://jobrxiv.org/job/uclouvain-27778-full-stack-sofware-engineer/?feed_id=77181

Looking at #tiledb for efficient storage and analysis of gene expression data, both #singlecell and #bulk. First port of call is a talk by @eddelbuettel.

Any other tutorials or real life use cases? Preferably using #aws #s3