The COnstraint-Based Reconstruction and Analysis Toolbox. Documentation:

Open-source data management for multimodal AI. Query, trace, and govern data with a lineage-native lakehouse for files, tables, arrays, ontologies, and notes. Supports biological data via bio-formats & registries by the creators of Scanpy. 🍊YC S22

Unified knowledge-driven network inference from omics data

Track, Analyze, Visualize: Unravel Your Microbiome's Temporal Pattern with MicrobiomeStat

Metabolic Engineering Workbench

Analyses for "State of the field in multi-omics research: from computational needs to data mining and sharing"

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

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

GenoCraft: A Comprehensive, User-Friendly Web Platform for High-Throughput Omics Data Analysis and Visualization (https://arxiv.org/pdf/2312.14249)

📦 Omics Data Analysis Tools

Genome-scale model of Yarrowia lipolytica.

profiler desktop versions

MicrobiomeStat Tutorial Repository: This is a comprehensive resource for learning how to use the MicrobiomeStat package. It provides a step-by-step guide to effectively analyze complex microbiome data.

Diversity-based enumeration of optimal context-specific metabolic networks

R package–style framework for correlation-based integration and visualization of multi-omics datasets

Potato ‘omics data analysis pipelines

Bayesian survival models for high-dimensional data

Modeling the metabolic changes during the epithelial-to-mesenchymal transition.

Metabolic Drug Repurposing Pipeline

Python package to preprocess and analyse multi-omics data