Scanpy

From https://anndata.readthedocs.io/en/latest/ "Python package for handling annotated data matrices in memory and on disk, positioned between pandas and xarray."

Programmatic data labeling and weak supervision

Python wrapper for [samtools](https://github.com/samtools/samtools).

A python-based workflow manager.

Pythonic access to FASTA files.

Probabilistic framework for inferring cell fate decisions and trajectory dynamics from multi-view single-cell data using Markov chains and machine learning, integrating RNA velocity, pseudotime, and metabolic labeling to predict differentiation paths and terminal states (scverse/Theis Lab, 449+ stars, BSD 3-Clause)