bowornpol/NUIM-pipeline

Network-based utility for integrating microbiome and metabolome data.

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RDA-MOMSI/Dashboard

MOMSI Standard Landscape Review Curation Workflow & Multi-Omics Dashboard

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jdutel42/MpBC_project

Spatial transcriptomics of MpBC. This project analyzes spatial transcriptomics data from 15 metaplastic breast carcinoma (MpBC) samples using 10x Genomics Visium. It aims to explore tumor heterogeneity and transdifferentiation, leveraging expert-labeled cell types to identify spatial clusters and biomarkers.

Language: Jupyter Notebook - Size: 650 MB - Last synced at: 12 days ago - Pushed at: 12 days ago - Stars: 0 - Forks: 0

opencobra/cobratoolbox

The COnstraint-Based Reconstruction and Analysis Toolbox. Documentation:

Language: MATLAB - Size: 1.64 GB - Last synced at: 5 days ago - Pushed at: 5 days ago - Stars: 263 - Forks: 330

Multiomics-Analytics-Group/acore

Functionality to preprocess and analyse multi-omics data

Language: Python - Size: 4.36 MB - Last synced at: 18 days ago - Pushed at: 18 days ago - Stars: 0 - Forks: 0

cafferychen777/MicrobiomeStat

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

Language: R - Size: 104 MB - Last synced at: 26 days ago - Pushed at: 26 days ago - Stars: 42 - Forks: 5

moonblume/GATv2-MultiOmics

Leveraging advanced graph neural networks to enhance the classification of bladder cancer subtypes by integrating multi-omics data

Language: Jupyter Notebook - Size: 4.84 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 0 - Forks: 0

pcastellanoescuder/POMA

:package: Omics Data Analysis Tools

Language: R - Size: 40.7 MB - Last synced at: 27 days ago - Pushed at: 8 months ago - Stars: 12 - Forks: 5

MetExplore/dexom-python

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

Language: Python - Size: 1.97 MB - Last synced at: 11 days ago - Pushed at: about 2 months ago - Stars: 1 - Forks: 0

futianfan/GenoCraft

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

Language: SCSS - Size: 69.9 MB - Last synced at: 2 months ago - Pushed at: 2 months ago - Stars: 17 - Forks: 1

qwerty239qwe/pipeGEM

This is a package for visualizing and analyzing multiple metabolic models. It also allow users to integrate omic data, metabolic tasks, and medium data with genome-scale metabolic models (GEMs).

Language: Python - Size: 9.4 MB - Last synced at: 21 days ago - Pushed at: 3 months 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: 178 MB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 5 - Forks: 2

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 at: 3 months ago - Pushed at: 3 months ago - Stars: 4 - Forks: 1

nara3m/nara3m

Nara Marella

Size: 80.1 KB - Last synced at: 4 months ago - Pushed at: 4 months ago - Stars: 1 - Forks: 0

MetExplore/dexom

Diversity-based enumeration of optimal context-specific metabolic networks

Language: MATLAB - Size: 2.32 MB - Last synced at: 4 months ago - Pushed at: about 4 years ago - Stars: 6 - Forks: 1

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 at: 3 months ago - Pushed at: about 2 years ago - Stars: 26 - Forks: 13

shashank-KU/OmniCorr

Calculate correlation between two omics data

Language: R - Size: 786 KB - Last synced at: 7 months ago - Pushed at: 7 months ago - Stars: 1 - Forks: 1

sriram-lab/emt-cobra

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

Language: HTML - Size: 78.1 MB - Last synced at: 6 months ago - Pushed at: 8 months ago - Stars: 3 - Forks: 1

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 at: 9 months ago - Pushed at: over 1 year ago - Stars: 21 - Forks: 11

selbouhaddani/PO2PLS

Probabilistic O2PLS

Language: R - Size: 3.03 MB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 2 - Forks: 3

ferdinand-popp/Deepan

Cluster patient based on their multiomics data utilizing graph autoencoders

Language: Python - Size: 287 KB - Last synced at: about 1 year ago - Pushed at: over 3 years ago - Stars: 1 - Forks: 0

ocbe-uio/BayesSurvive

Bayesian survival models for high-dimensional data

Language: R - Size: 903 KB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 1

babessell1/MADRID Fork of HelikarLab/COMO

Metabolic Drug Repurposing Pipeline

Language: Python - Size: 733 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 4 - Forks: 0

BioSystemsUM/MEWpy

Metabolic Engineering Workbench

Language: Python - Size: 28.6 MB - Last synced at: over 1 year ago - Pushed at: almost 2 years ago - Stars: 34 - Forks: 11

crhisto/DecoFlex

DecoFlex deconvolution method for Omic data implemented as DecoFlexR

Language: R - Size: 8.81 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 0

SysBioChalmers/Yarrowia_lipolytica_W29-GEM

Genome-scale model of Yarrowia lipolytica.

Language: MATLAB - Size: 3.61 MB - Last synced at: 23 days ago - Pushed at: almost 4 years ago - Stars: 8 - Forks: 8

ngiangre/ROMOPOmics Fork of AndrewC160/ROMOPOmics

R package to parse datasets into SQLite-friendly tables

Language: R - Size: 2.75 MB - Last synced at: 1 day ago - Pushed at: about 4 years ago - Stars: 1 - Forks: 0

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 at: over 1 year ago - Pushed at: over 1 year 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 at: almost 2 years ago - Pushed at: over 4 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 at: almost 2 years ago - Pushed at: almost 2 years ago - Stars: 1 - Forks: 0

annkamsk/mvae

Multimodal Variational Autoencoder dedicated to omics data integration

Language: Jupyter Notebook - Size: 544 MB - Last synced at: about 2 years ago - Pushed at: about 2 years ago - Stars: 0 - Forks: 0

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 at: almost 2 years ago - Pushed at: about 3 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 at: about 2 years ago - Pushed at: over 2 years ago - Stars: 1 - 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 at: over 2 years ago - Pushed at: over 4 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 at: over 2 years ago - Pushed at: almost 3 years ago - Stars: 0 - Forks: 0

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 at: over 2 years ago - Pushed at: about 3 years ago - Stars: 0 - Forks: 0

mbongaerts/Reafect

Language: Jupyter Notebook - Size: 1.73 MB - Last synced at: over 2 years ago - Pushed at: about 3 years ago - Stars: 0 - Forks: 0

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

data analytics & machine learning meet genetics @ AUC

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gpalou4/TFM

"DNA methylation and gene expression integration in cardiovascular disease"

Language: R - Size: 495 MB - Last synced at: about 1 month ago - Pushed at: over 4 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 at: 5 months ago - Pushed at: about 3 years ago - Stars: 0 - Forks: 1