Omics Data Integration Python Packages

lamindb

Open-source data management for multimodal AI. Query, trace, and govern with a lineage-native, format-agnostic lakehouse for agents and teams. Supports biological formats and registries - by the creators of Scanpy. 🍊YC S22

lamindb-core

Open-source data management for multimodal AI. Query, trace, and govern with a lineage-native, format-agnostic lakehouse for agents and teams. Supports biological formats and registries - by the creators of Scanpy. 🍊YC S22

thyra

A modern Python library for converting Mass Spectrometry Imaging (MSI) data into standardized SpatialData/Zarr format, enabling seamless integration with spatial omics analysis workflows.

corneto

Unified knowledge-driven network inference from omics data

acore

Python package to preprocess and analyse multi-omics data

amon-bio

Annotation of Metabolite Origin via Networks: A tool for predicting putative metabolite origins for microbes or between microbes and host with or without metabolomics data

mcp-genelab

A Model Context Protocol (MCP) server for querying Neo4j Graph Databases with customized tools to query the NASA GeneLab Knowledge Graph