Multi Omics Python Packages

mudata

Multimodal Data (.h5mu) implementation for Python

muon

muon is a multimodal omics Python framework

graphvelo

Inferring manifold-constrained velocity and transforming vectors across representations

pymultiomics

Python toolbox for multi-omics data mapping and analysis

gnnsubnet

Disease subnetwork detection with explainable Graph Neural Networks

mofaflex

factor models for omics data

mudatasets

Multimodal datasets, in MuData format

pymaftools

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

move-dl

Multi-omics variational autoencoder

modos

Python API to manage multi-omics digital objects

maui-tools

Multi-omics Autoencoder Integration

autoencodix

Framework for multi-omics data integration by autoencoders.

openomics

OpenOmics provides a bioinformatics API and web-app platform integrate and visualize the multiomics and clinical data.

platygeno

Unsupervised Gene Discovery via Evo 2 & SAE Interpretability

ymp

Flexible multi-omic pipeline system

neticspy

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

monti

MONTI is a tool for analyzing large multi-omics cancer cohort data in association with clinical featuers

scotch-sc

SCOTCH is a Single-Cell multi-modal integration method leveraging the Optimal Transport algorithm and a cell matCHing strategy