The COnstraint-Based Reconstruction and Analysis Toolbox. Documentation:

Open-source data framework for biology. Context and memory for datasets and models at scale. Query, trace & validate with a lineage-native lakehouse that supports bio-formats, registries & ontologies. 🍊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

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

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

:package: Omics Data Analysis Tools

profiler desktop versions

Genome-scale model of Yarrowia lipolytica.

Diversity-based enumeration of optimal context-specific metabolic networks

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.

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

GitHub Repository associated with the piQTL project (Mapping effects of genome-wide genetic variation to protein-protein interactions reveals molecular mechanisms of complex traits) [ Serohijos & Michnick Lab, Université de Montréal ]

Bayesian survival models for high-dimensional data

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

Probabilistic O2PLS

IgemRNA is an open access toolbox for transcriptome data statistical and biochemical network topology-based analysis. IgemRNA was developed in the MATLAB environment in order to take advantage of the up-to-date and most commonly distributed GSM modelling tool Cobra Toolbox 3.0 and spreadsheet file capabilities.

TBN_learning is a MATLAB implemented hybrid algorithm for learning the structure of transcriptional Bayesian networks on a genome-wide scale.

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

Potato ‘omics data analysis pipelines

Curated list of analysis pipelines for biological & clinical interpretation of data-driven findings

Code to reproduce preprocessing analysis of IBD dataset from the Human Microbiome Project. This work will provide a walk through analysis tool for the scientific community with less technical knowledge on data science and machine learning.

DecoFlex deconvolution method for Omic data implemented as DecoFlexR

Constraint-based metabolic modeling software from the Chandrasekaran Lab

Functionality to preprocess and analyse multi-omics data

This repository is the code source for the RegOmics tool - Regulatory extraction for Omics data.

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