Human Cell Atlas Python Packages

scvi-tools

Deep probabilistic analysis of single-cell and spatial omics data

starfish

starfish: unified pipelines for image-based transcriptomics

scarches

Reference mapping for single-cell genomics

zappy

Distributed processing with NumPy and Zarr

scvi

Deep probabilistic analysis of single-cell and spatial omics data

single-cell-portal

Tutorials, workflows, and convenience scripts for Single Cell Portal

genes2genes

Aligning gene expression trajectories of single-cell reference and query systems