Multi Omics Python Packages

mudata

Multimodal Data (.h5mu) implementation for Python

muon

muon is a multimodal omics Python framework

biomedical-ai-skills

AI agent skills for cancer biology and multi-omics research

pymultiomics

Python toolbox for multi-omics data mapping and analysis

gnnsubnet

Disease subnetwork detection with explainable Graph Neural Networks

bioconverge

Python framework for biological score integration, patient stratification, concordance analysis, archetype discovery, and validation-aware computational biology.

graphvelo

Inferring multi-modality dynamics for single cell genomics data

mofaflex

factor models for omics data

autoencodix

Python library for multi-omics data integration by autoencoders

pymaftools

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

move-dl

MOVE (Multi-Omics Variational autoEncoder) for integrating multi-omics data and identifying cross modal associations

omicau

Omics Audit: reproducible, leakage-safe multi-omics data-audit and fusion-benchmarking CLI.

maui-tools

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

modos

Python API to manage multi-omics digital objects

ymp

Flexible omics pipeline

openomics

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

intelligrate

Diversity-aware sample selection and kNN-based extrapolation of a partially measured data layer to the complete dataset.

platygeno

PlatyGeno is a Python package for identifying genomic landmarks directly from raw sequence data. By leveraging the Evo 2 foundation model, it performs annotation-independent identification of biologically significant structures—such as promoters, coding sequences, and precise motifs—relying purely on model confidence and latent feature.

neticspy

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

mudatasets

Multimodal datasets, in MuData format

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