← Single-cell & foundation models

MuData / muon

Multimodal omics framework for single-cell multi-omics in Python.

Visit website ↗

CategorySingle-cell & foundation models
GitHubscverse/muon
First public2021-06-01 (source)
Paperhttps://genomebiology.biomedcentral.com/articles/10.1186/s13059-021-02577-8 · Genome Biology (2022)
LicenseBSD-3-Clause
PricingOpen source
Tags#multimodal#scverse
Last checked2026-10-16

Specs

Pretraining corpusN/A (analysis framework)
ArchitecturePython framework on MuData/AnnData
TasksMultimodal omics analysis (e.g. RNA + ATAC)
Species—
GitHub stars280
Interface—

Specs come from each project's README, paper or official page · MuData / muon README. “—” means we couldn't verify it.

Compare with…

Pick 1–3 other Single-cell & foundation models tools to compare side by side with MuData / muon.

Select 1–3 tools

Related

Seurat

R toolkit for single-cell genomics, integration and multimodal analysis.

Single-cell & foundation modelsOpen source#r#integration

Scanpy

Scalable Python toolkit for single-cell gene expression analysis.

Single-cell & foundation modelsOpen source#python#scverse

scvi-tools

Probabilistic deep generative models for single-cell omics (scVI, totalVI, scANVI...).

Single-cell & foundation modelsOpen source#vae#integration