opencobra/cobratoolbox

The COnstraint-Based Reconstruction and Analysis Toolbox. Documentation:

Language: MATLAB - Size: 1.02 GB - Last synced: about 7 hours ago - Pushed: about 7 hours ago - Stars: 237 - Forks: 302

cafferychen777/MicrobiomeStat

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

Language: R - Size: 15.6 MB - Last synced: about 19 hours ago - Pushed: about 20 hours ago - Stars: 24 - Forks: 3

nara3m/nara3m

Nara Marella

Size: 30.3 KB - Last synced: 3 days ago - Pushed: 3 days ago - Stars: 0 - Forks: 0

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.

Size: 176 MB - Last synced: 5 days ago - Pushed: 6 days ago - Stars: 2 - Forks: 2

ocbe-uio/BayesSurvive

Bayesian survival models for high-dimensional data

Language: R - Size: 903 KB - Last synced: 9 days ago - Pushed: 9 days ago - Stars: 0 - Forks: 1

babessell1/MADRID Fork of HelikarLab/COMO

Metabolic Drug Repurposing Pipeline

Language: Python - Size: 733 MB - Last synced: 7 days ago - Pushed: 7 days ago - Stars: 4 - Forks: 0

futianfan/GenoCraft

GenoCraft: A Comprehensive, User-Friendly Web-Based Platform for High-Throughput Omics Data Analysis and Visualization

Language: SCSS - Size: 68.2 MB - Last synced: 7 days ago - Pushed: 11 days ago - Stars: 13 - Forks: 0

BioSystemsUM/MEWpy

Metabolic Engineering Workbench

Language: Python - Size: 28.6 MB - Last synced: 6 days ago - Pushed: 9 months ago - Stars: 34 - Forks: 11

pcastellanoescuder/POMA

:package: Tools for Omics Data Analysis

Language: R - Size: 40.7 MB - Last synced: about 2 months ago - Pushed: about 2 months ago - Stars: 9 - Forks: 5

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

Language: Python - Size: 105 KB - Last synced: 13 days ago - Pushed: 13 days ago - Stars: 20 - Forks: 11

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"

Language: Jupyter Notebook - Size: 16.6 MB - Last synced: 16 days ago - Pushed: 10 months ago - Stars: 23 - Forks: 10

crhisto/DecoFlex

DecoFlex deconvolution method for Omic data implemented as DecoFlexR

Language: R - Size: 8.81 MB - Last synced: about 2 months ago - Pushed: about 2 months ago - Stars: 0 - Forks: 0

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 ]

Language: Jupyter Notebook - Size: 1.72 GB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 4 - Forks: 1

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.

Language: R - Size: 4.88 KB - Last synced: 3 months ago - Pushed: 5 months ago - Stars: 0 - Forks: 0

sriram-lab/metabolicmodeling

Constraint-based metabolic modeling software from the Chandrasekaran Lab

Language: HTML - Size: 22.8 MB - Last synced: 6 months ago - Pushed: about 3 years ago - Stars: 2 - Forks: 2

NhanNguyen000/RegOmics

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

Language: R - Size: 15.6 MB - Last synced: 8 months ago - Pushed: 8 months ago - Stars: 1 - Forks: 0

SysBioChalmers/Yarrowia_lipolytica_W29-GEM

Genome-scale model of Yarrowia lipolytica.

Language: MATLAB - Size: 3.61 MB - Last synced: 6 months ago - Pushed: over 2 years ago - Stars: 7 - Forks: 7

MetExplore/dexom-python

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

Language: Python - Size: 1.61 MB - Last synced: about 2 months ago - Pushed: about 2 months ago - Stars: 2 - Forks: 0

annkamsk/mvae

Multimodal Variational Autoencoder dedicated to omics data integration

Language: Jupyter Notebook - Size: 544 MB - Last synced: 10 months ago - Pushed: 10 months ago - Stars: 0 - Forks: 0

selbouhaddani/PO2PLS

Probabilistic O2PLS

Language: R - Size: 3.03 MB - Last synced: 2 months ago - Pushed: 2 months ago - Stars: 2 - Forks: 3

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.

Language: MATLAB - Size: 16.2 MB - Last synced: 6 months ago - Pushed: almost 2 years ago - Stars: 2 - Forks: 1

MendenLab/miRNAInt_Ferroptosis

Multi-omics differential expression and integration using PPI networks

Language: R - Size: 2.79 MB - Last synced: 11 months ago - Pushed: about 1 year ago - Stars: 1 - Forks: 0

shashank-KU/OmniCorr

Calculate correlation between two omics data

Language: R - Size: 841 KB - Last synced: 7 months ago - Pushed: 7 months ago - Stars: 0 - Forks: 0

ScottCampit/single-cell-neutrophil-flux-analysis Fork of sriram-lab/single-cell-neutrophil-flux-analysis

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

Size: 14.1 MB - Last synced: about 1 year ago - Pushed: about 3 years ago - Stars: 0 - Forks: 0

ikmb/OmLiT

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

Language: Rust - Size: 6.66 MB - Last synced: about 1 year ago - Pushed: over 1 year ago - Stars: 0 - Forks: 0

sriram-lab/emt-cobra

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

Language: HTML - Size: 78.1 MB - Last synced: about 1 year ago - Pushed: over 1 year ago - Stars: 2 - Forks: 1

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.

Language: Jupyter Notebook - Size: 2.94 MB - Last synced: about 1 year ago - Pushed: almost 2 years ago - Stars: 0 - Forks: 0

mbongaerts/Reafect

Language: Jupyter Notebook - Size: 1.73 MB - Last synced: about 1 year ago - Pushed: almost 2 years ago - Stars: 0 - Forks: 0

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

data analytics & machine learning meet genetics @ AUC

Language: JavaScript - Size: 7.21 MB - Last synced: about 1 year ago - Pushed: almost 2 years ago - Stars: 0 - Forks: 7

MetExplore/dexom

Diversity-based enumeration of optimal context-specific metabolic networks

Language: MATLAB - Size: 2.32 MB - Last synced: 6 months ago - Pushed: almost 3 years ago - Stars: 5 - Forks: 1

ngiangre/ROMOPOmics Fork of AndrewC160/ROMOPOmics

R package to parse datasets into SQLite-friendly tables

Language: R - Size: 2.75 MB - Last synced: about 1 year ago - Pushed: almost 3 years ago - Stars: 0 - Forks: 0

krassowski/meningitis-integration

Discovering biomarkers for meningitis by multivariate integration of multi-omics and clinical data

Language: Jupyter Notebook - Size: 103 MB - Last synced: 16 days ago - Pushed: almost 2 years ago - Stars: 0 - Forks: 1