The COnstraint-Based Reconstruction and Analysis Toolbox. Documentation:

Metabolic Engineering Workbench

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

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)

📦 Omics Data Analysis Tools

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.

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 ]

Metabolic Drug Repurposing Pipeline

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

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.

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

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

Probabilistic O2PLS

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.

Constraint-based metabolic modeling software from the Chandrasekaran Lab

Multi-omics differential expression and integration using PPI networks