RHRJ Honickyinlearning-exhaust.hashnode.dev·Jan 12 · 13 min readIntroducing 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...00
RHRJ Honickyinlearning-exhaust.hashnode.dev·Jul 28, 2025 · 10 min readLab 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...00
RHRJ Honickyinlearning-exhaust.hashnode.dev·Jul 5, 2025 · 7 min readLab 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...00
RHRJ Honickyinlearning-exhaust.hashnode.dev·Jun 28, 2025 · 5 min readLab 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...00
RHRJ Honickyinlearning-exhaust.hashnode.dev·Mar 5, 2025 · 9 min readLab 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...00
