There are 2 repositories under omics-data-integration topic.
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
:package: Omics Data Analysis Tools
Genome-scale model of Yarrowia lipolytica.
Diversity-based enumeration of optimal context-specific metabolic networks
Metabolic Drug Repurposing Pipeline
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 ]
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.
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.
Modeling the metabolic changes during the epithelial-to-mesenchymal transition.
TBN_learning is a MATLAB implemented hybrid algorithm for learning the structure of transcriptional Bayesian networks on a genome-wide scale.
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.
Probabilistic O2PLS
Constraint-based metabolic modeling software from the Chandrasekaran Lab
Analysis of proteomics datasets obtained from ChIP-SICAP experiments in HEK cells
Cluster patient based on their multiomics data utilizing graph autoencoders
Multi-omics differential expression and integration using PPI networks
diversity-based enumeration of optimal context-specific metabolic networks using the cobrapy library
R package to parse datasets into SQLite-friendly tables
This repository is the code source for the RegOmics tool - Regulatory extraction for Omics data.
Bayesian survival models for high-dimensional data
Calculate correlation between two omics data
Code for Zhang, Wei, Slowikowski, Fonseka, Rao, et al, Nature Immunology, 2019. Single-cell transcriptomics and proteomics data analysis and integration for rheumatoid arthritis synovial tissue. These integrative strategies can be generalized to any other diseases.
MOFA (Multi-Omics Factor Analysis) is a computational framework and statistical method designed for the integration and analysis of multi-omics data.
Analysis of neutrophil metabolic activity during metastasis using single-cell RNASeq and COnstraint-Based Reconstruction and Analysis.
data analytics & machine learning meet genetics @ AUC
A Rust accelerated library for annotation and preparing multi-omics data for training deep learning models