omics-data-integration

cafferychen777/MicrobiomeStat

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

BioSystemsUM/MEWpy

Metabolic Engineering Workbench

krassowski/multi-omics-state-of-the-field

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

lozuponelab/AMON

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

futianfan/GenoCraft

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

pcastellanoescuder/POMA

:package: Omics Data Analysis Tools

SysBioChalmers/Yarrowia_lipolytica_W29-GEM

Genome-scale model of Yarrowia lipolytica.

cafferychen777/MicrobiomeStat-Turtorial-Professional-Version

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.

MetExplore/dexom

Diversity-based enumeration of optimal context-specific metabolic networks

babessell1/MADRID

Metabolic Drug Repurposing Pipeline

ladyson1806/SerohijosLab-piQTL

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 ]

BigDataInSilicoBiologyGroup/IgemRNA

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.

esauta/TBN_learning

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

sriram-lab/emt-cobra

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

akatrib/sys-bio

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

muia2021pl/Preprocessing_HumanMicrobiome

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.

selbouhaddani/PO2PLS

Probabilistic O2PLS

shashank-KU/OmniCorr

Calculate correlation between two omics data

sriram-lab/metabolicmodeling

Constraint-based metabolic modeling software from the Chandrasekaran Lab

adityamahadevaniyer/ChIP-SICAP

Analysis of proteomics datasets obtained from ChIP-SICAP experiments in HEK cells

annkamsk/mvae

Multimodal Variational Autoencoder dedicated to omics data integration

crhisto/DecoFlex

DecoFlex deconvolution method for Omic data implemented as DecoFlexR

ferdinand-popp/Deepan

Cluster patient based on their multiomics data utilizing graph autoencoders

mbongaerts/Reafect

MendenLab/miRNAInt_Ferroptosis

Multi-omics differential expression and integration using PPI networks

MetExplore/dexom-python

diversity-based enumeration of optimal context-specific metabolic networks using the cobrapy library

nara3m/nara3m

Nara Marella

ngiangre/ROMOPOmics

R package to parse datasets into SQLite-friendly tables

NhanNguyen000/RegOmics

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

fanzhanglab/amp_phase1_ra

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.

ocbe-uio/BayesSurvive

Bayesian survival models for high-dimensional data

saifeldeen-bio/MultiOmics

MOFA (Multi-Omics Factor Analysis) is a computational framework and statistical method designed for the integration and analysis of multi-omics data.

ScottCampit/single-cell-neutrophil-flux-analysis

Analysis of neutrophil metabolic activity during metastasis using single-cell RNASeq and COnstraint-Based Reconstruction and Analysis.

systems-genomics-lab-auc/systems-genomics-lab.github.io

data analytics & machine learning meet genetics @ AUC

ikmb/OmLiT

A Rust accelerated library for annotation and preparing multi-omics data for training deep learning models