Multi Omics Python Packages

mudata

Multimodal Data (.h5mu) implementation for Python

muon

muon is a multimodal omics Python framework

gnnsubnet

Disease subnetwork detection with explainable Graph Neural Networks

graphvelo

Inferring multi-modality dynamics for single cell genomics data

pymultiomics

Python toolbox for multi-omics data mapping and analysis

mofaflex

factor models for omics data

autoencodix

Python library for multi-omics data integration by autoencoders

move-dl

Multi-omics variational autoencoder

mudatasets

Multimodal datasets, in MuData format

platygeno

Unsupervised Gene Discovery via Evo 2 & SAE Interpretability

modos

SMOC Multi-Omics Digital Object System API

openomics

A bioinformatics API to interface with public multi-omics bio databases for wicked fast data integration.

maui-tools

Multi-omics Autoencoder Integration: Deep learning-based heterogenous data analysis toolkit

pymaftools

A Python toolkit for MAF files and multi-omics cancer genomics — parsing, analysis, ML, and publication-ready visualization.

ymp

Flexible multi-omic pipeline system

neticspy

Python implementation of NetICS (Network-based Integration of Multi-omics data).

monti

A multi-omics integrative analysis tool

scotch-sc

SCOTCH: Single-Cell multi-modal integration using Optimal Transport and Cell matCHing