learning-exhaust.hashnode.devIntroducing the AnnData DuckDB extensionAt MiraOmics we look at a lot of H5AD files. We have a database of over a thousand of them, not to mention several of the public data sources. Pretty much every time I have a new file, the first thing I want to do is run a few queries on it to under...Jan 12·13 min read
learning-exhaust.hashnode.devLab Notes: Building a GenePT Cell Typer - Part 3Introduction We recently built a cell-typer model based on a subset of the CellXGene V2 dataset. This model is a stepping stone towards a “universal” cell-typer model that will allow us to annotate cell types (and other properties) based on single ce...Jul 28, 2025·10 min read
learning-exhaust.hashnode.devLab Notes: Building a GenePT Cell Typer - Part 2Introduction We recently built a cell-typer model based on a subset of the CellXGene V2 dataset. This model is a stepping stone towards a “universal” cell-typer model that will allow us to annotate cell types (and other properties) based on single ce...Jul 5, 2025·7 min read
learning-exhaust.hashnode.devLab Notes: Building a GenePT Cell Typer - Part 1Introduction We recently built a cell-typer model based on a subset of the CellXGene V2 dataset. This model is a stepping stone towards a “universal” cell-typer model that will allow us to annotate cell types (and other properties) based on single ce...Jun 28, 2025·5 min read
learning-exhaust.hashnode.devLab Notes: Custom GenePT embeddingsIn the spirit of “Learning in Public,” and “learning exhaust,” I’m adding “Lab Notes” blog posts that chronicle little discoveries or failures that I have along the way to a larger goal. This is a followup to my previous Lab Notes: Comparing GenePT a...Mar 5, 2025·9 min read
