muon is a multimodal omics Python framework
Conversational & memory-enabled AI research partner for multi-omics analysis. CLI + Desktop App (installers in Releases). From biological idea to full research paper.
Multimodal Data (.h5mu) implementation for Python
Single-cell multi-omics integration using Optimal Transport
Multi-task deep learning framework for multi-omics data analysis
HiCFoundation is a generalizable Hi-C foundation model for chromatin architecture, single-cell and multi-omics analysis across species.
factor models for omics data
A bioinformatics API to interface with public multi-omics bio databases for wicked fast data integration.
Disease subnetwork detection with explainable Graph Neural Networks
molly, an LLM designed to understand multi-omics data.
Flexible omics pipeline
gNOMO2 allows integrated multi-omics analyses of microbiomes
A Python toolkit for MAF files and multi-omics cancer genomics — parsing, analysis, ML, and publication-ready visualization.
The #1 open-source collection of scientific AI Agent Skills, tool specifications, and prompt protocols for Bioinformatics, Genomics, Drug Discovery, and Multi-Omics. Compatible with Cursor, Claude Code, Antigravity, and LangChain.
Accompanying code for Image2Omics
The SUbgraph BAsed mulTI-OMIcs Clustering (SUBATOMIC) framework infers interpretable modules with a specific topology.
Data and scripts to reproduce experiments for Mowgli.
DeepResponse: Large Scale Prediction of Cancer Cell Line Drug Response with Deep Learning Based Pharmacogenomic Modelling
Multimodal datasets, in MuData format
A curated list of state-of-the-art multi-omics tools, pipelines, databases, and papers covering transcriptomics, single-cell, spatial omics, and epigenomics.
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