anndata
Category: life-sciences · License: BSD-3-Clause license · Version: 1.2
Tags: single-cell, h5ad, scverse, bioinformatics, data formats
When to use it
Data structure for annotated matrices in single-cell analysis. Use when working with .h5ad files or integrating with the scverse ecosystem. This is the data format skill—for analysis workflows use scanpy; for probabilistic models use scvi-tools; for population-scale queries use cellxgene-census.Example requests
Ask your agent in plain language, for example:- “How do I read a .h5ad file in backed mode so it doesn’t load into RAM?”
- “I have three batches saved as batch1.h5ad, batch2.h5ad and batch3.h5ad with different gene panels. I ran
adata1.concatenate(adata2, adata3)and got a FutureWarning, and the result is missing a lot of genes. How do I combine them properly, keep track of which batch each cell came from, and keep the union of genes?” - “I’ve got a cell-by-gene count matrix in a CSV, a separate table of cell metadata (donor, tissue, sequencing run), and a gene annotation table. I want to bundle everything into one object that I can slice by cell or gene and save as a single file for collaborators in the scverse ecosystem. How should I set that up?”
Install
/plugin marketplace add KalarisLabs/research-agent-skills and install the whole life-sciences category with /plugin install life-sciences@research-agent-skills.