Single-cell analysis in Python. Scales to >100M cells.

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.

Annotated data.

A Python implementation of the DESeq2 pipeline for bulk RNA-seq DEA.

Spatial Single Cell Analysis in Python

CellRank: dynamics from multi-view single-cell data

rapids-singlecell: GPU-accelerated framework for scRNA analysis