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

Deep probabilistic analysis of single-cell and spatial omics data

Annotated data.

rapids-singlecell: GPU-accelerated framework for scRNA analysis

An open and interoperable data framework for spatial omics data

Electronic Health Record Analysis with Python.

Single-cell perturbation analysis

Python package to perform enrichment analysis from omics data.

muon is a multimodal omics Python framework

A scanpy extension to analyse single-cell TCR and BCR data.

Infer copy number variation (CNV) from scRNA-seq data. Plays nicely with Scanpy.

Multimodal Data (.h5mu) implementation for Python

A single cell transcriptomics pipeline for QC, integration and making the data presentable

Accelerated, Python-only, single-cell integration benchmarking metrics

CREsted is a Python package for training sequence-based deep learning models on scATAC-seq data, for capturing enhancer code and for designing cell type-specific sequences.

Notebooks used in scvi-tools tutorials

Feature-rich Python implementation of the tximport package for gene count estimation.

BioContextAI Knowledgebase MCP server for biomedical agentic AI

Muon for Julia

Search- and quantification-engine agnostic biological interpretation of proteomics data