Topic: "omics-data-integration"
opencobra/cobratoolbox
The COnstraint-Based Reconstruction and Analysis Toolbox. Documentation:
Language: MATLAB - Size: 1.59 GB - Last synced at: 16 days ago - Pushed at: 16 days ago - Stars: 261 - Forks: 323
cafferychen777/MicrobiomeStat
Track, Analyze, Visualize: Unravel Your Microbiome's Temporal Pattern with MicrobiomeStat
Language: R - Size: 119 MB - Last synced at: 8 days ago - Pushed at: 12 days ago - Stars: 40 - Forks: 5
BioSystemsUM/MEWpy
Metabolic Engineering Workbench
Language: Python - Size: 28.6 MB - Last synced at: about 1 year ago - Pushed at: over 1 year ago - Stars: 34 - 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 at: 4 days ago - Pushed at: almost 2 years ago - Stars: 26 - Forks: 13
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: 6 months ago - Pushed at: about 1 year ago - Stars: 21 - Forks: 11
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: 6 months ago - Pushed at: 6 months ago - Stars: 14 - Forks: 0
pcastellanoescuder/POMA
:package: Tools for Omics Data Analysis
Language: R - Size: 40.7 MB - Last synced at: 12 months ago - Pushed at: about 1 year ago - Stars: 10 - Forks: 5
SysBioChalmers/Yarrowia_lipolytica_W29-GEM
Genome-scale model of Yarrowia lipolytica.
Language: MATLAB - Size: 3.61 MB - Last synced at: 19 days ago - Pushed at: over 3 years ago - Stars: 8 - Forks: 8
MetExplore/dexom
Diversity-based enumeration of optimal context-specific metabolic networks
Language: MATLAB - Size: 2.32 MB - Last synced at: 17 days ago - Pushed at: almost 4 years ago - Stars: 6 - Forks: 1
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 days ago - Pushed at: 3 days ago - Stars: 4 - Forks: 1
babessell1/MADRID Fork of HelikarLab/COMO
Metabolic Drug Repurposing Pipeline
Language: Python - Size: 733 MB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 4 - Forks: 0
sriram-lab/emt-cobra
Modeling the metabolic changes during the epithelial-to-mesenchymal transition.
Language: HTML - Size: 78.1 MB - Last synced at: 3 months ago - Pushed at: 5 months ago - Stars: 3 - Forks: 1
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 at: 7 months ago - Pushed at: 7 months ago - Stars: 3 - Forks: 2
selbouhaddani/PO2PLS
Probabilistic O2PLS
Language: R - Size: 3.03 MB - Last synced at: 10 months ago - Pushed at: 10 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 at: over 1 year ago - Pushed at: almost 3 years ago - Stars: 2 - Forks: 1
sriram-lab/metabolicmodeling
Constraint-based metabolic modeling software from the Chandrasekaran Lab
Language: HTML - Size: 22.8 MB - Last synced at: over 1 year ago - Pushed at: about 4 years ago - Stars: 2 - Forks: 2
MetExplore/dexom-python
diversity-based enumeration of optimal context-specific metabolic networks using the cobrapy library
Language: Python - Size: 1.93 MB - Last synced at: about 1 hour ago - Pushed at: 13 days ago - Stars: 1 - Forks: 0
nara3m/nara3m
Nara Marella
Size: 80.1 KB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 1 - Forks: 0
shashank-KU/OmniCorr
Calculate correlation between two omics data
Language: R - Size: 786 KB - Last synced at: 4 months ago - Pushed at: 4 months ago - Stars: 1 - Forks: 1
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: over 1 year ago - Pushed at: over 1 year ago - Stars: 1 - Forks: 0
MendenLab/miRNAInt_Ferroptosis
Multi-omics differential expression and integration using PPI networks
Language: R - Size: 2.79 MB - Last synced at: almost 2 years ago - Pushed at: about 2 years ago - Stars: 1 - Forks: 0
ferdinand-popp/Deepan
Cluster patient based on their multiomics data utilizing graph autoencoders
Language: Python - Size: 287 KB - Last synced at: 11 months ago - Pushed at: about 3 years ago - Stars: 1 - Forks: 0
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: almost 4 years ago - Stars: 1 - Forks: 0
RDA-MOMSI/Dashboard
MOMSI WG Landscape Review Dashboard
Language: JavaScript - Size: 5.4 MB - Last synced at: 5 days ago - Pushed at: 5 days ago - Stars: 0 - Forks: 0
Multiomics-Analytics-Group/acore
Functionality to preprocess and analyse multi-omics data
Language: Python - Size: 2.83 MB - Last synced at: 12 days ago - Pushed at: about 1 month ago - Stars: 0 - Forks: 0
ocbe-uio/BayesSurvive
Bayesian survival models for high-dimensional data
Language: R - Size: 903 KB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 0 - Forks: 1
crhisto/DecoFlex
DecoFlex deconvolution method for Omic data implemented as DecoFlexR
Language: R - Size: 8.81 MB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 0 - 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: about 1 year ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 0
annkamsk/mvae
Multimodal Variational Autoencoder dedicated to omics data integration
Language: Jupyter Notebook - Size: 544 MB - Last synced at: almost 2 years ago - Pushed at: almost 2 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: about 2 years ago - Pushed at: over 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 at: about 2 years ago - Pushed at: almost 3 years ago - Stars: 0 - Forks: 7
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: about 2 years ago - Pushed at: 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 at: about 2 months ago - Pushed at: almost 3 years ago - Stars: 0 - Forks: 1
mbongaerts/Reafect
Language: Jupyter Notebook - Size: 1.73 MB - Last synced at: about 2 years ago - Pushed at: almost 3 years 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 at: about 2 years ago - Pushed at: about 4 years ago - Stars: 0 - Forks: 0
