omics-data-integration

There are 3 repositories under omics-data-integration topic.

opencobra / cobratoolbox
The COnstraint-Based Reconstruction and Analysis Toolbox. Documentation:
cobra-toolbox reconstruction tutorial metabolic-models metabolic-reconstruction metabolic-engineering gap-filling strain-engineering omics-data-integration metabolomics transcriptomics cobra constraint-based-modeling human-metabolism microbiome-analysis
Language:MATLAB 269
cafferychen777 / MicrobiomeStat
Track, Analyze, Visualize: Unravel Your Microbiome's Temporal Pattern with MicrobiomeStat
16s-rrna amplicon-sequencing dada2 longitudinal-data metagenomes metagenomic-analysis microbiome microbiome-analysis microbiome-data phyloseq qiime2 statistics visualization microbiome-workflow omics omics-data-integration
Language:R 47
BioSystemsUM / MEWpy
Metabolic Engineering Workbench
strain optimization kinetic-modeling microbial-communities modeling omics-data-integration python simulation
Language:Python 40
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"
multi-omics binder-ready integrative-omics omics omics-data-integration papers-with-code
Language:Jupyter Notebook 28
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
microbiome metabolome bioinformatics omics-data-integration
Language:Python 23
futianfan / GenoCraft
GenoCraft: A Comprehensive, User-Friendly Web Platform for High-Throughput Omics Data Analysis and Visualization (https://arxiv.org/pdf/2312.14249)
bulk-rna-seq flask genomics multiomics next-generation-sequencing ngs omics omics-data-integration pathway-analysis protein rna-seq single-cell visualization
Language:SCSS 19
pcastellanoescuder / POMA
:package: Omics Data Analysis Tools
statistical-analysis r r-package bioinformatics workflow pipeline bioconductor data-visualization user-friendly exploratory-data-analysis pre-processing dimension-reduction machine-learning omics-data-integration rstats
Language:R 13
SysBioChalmers / Yarrowia_lipolytica_W29-GEM
Genome-scale model of Yarrowia lipolytica.
yarrowia-lipolytica metabolic-engineering metabolic-reconstruction systems-biology stoichiometric-reactions omics-data-integration constraint-based-modeling metabolic-models metabolic-network genome-scale-models
Language:MATLAB 10
Tomatokeftes / thyra
A modern Python library for converting Mass Spectrometry Imaging (MSI) data into standardized SpatialData/Zarr format, enabling seamless integration with spatial omics analysis workflows.
bioinformatics bruker data-conversion imzml mass-spectrometry mass-spectrometry-imaging msi omics-data-integration scientific-computing spatial-omics spatialdata zarr
Language:Python 9
MetExplore / dexom
Diversity-based enumeration of optimal context-specific metabolic networks
metabolic-network metabolic-reconstruction metabolic-engineering metabolic-pathways metabolism constraint-based-modeling optimization cobra-toolbox omics-data-integration
Language:MATLAB 7
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.
16s 16s-rrna 16s-seq analysis data-analysis metagenomes metagenomic-analysis metagenomic-pipeline metagenomics microbiome microbiome-analysis microbiome-analysis-pipelines microbiome-data microbiome-workflow omics omics-data omics-data-analysis omics-data-integration visualization
6
babessell1 / MADRID
Metabolic Drug Repurposing Pipeline
metabolism omics-data omics-data-integration constraint-based-modeling transcriptomics proteomics pipeline drug-repurposing drug-discovery
Language:Python 4
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 ]
bioinformatics biological-networks gwas omics-data-integration population-genetics protein-protein-interaction-network qtl-mapping systems-biology yeast gene-interaction-network
Language:Jupyter Notebook 4
ocbe-uio / BayesSurvive
Bayesian survival models for high-dimensional data
bayesian-cox-models bayesian-variable-selection graph-learning high-dimensional-statistics omics-data-integration survival-analysis
Language:R 4
shashank-KU / OmniCorr
Calculate correlation between two omics data
correlation data-visualization omics-data-integration r
Language:R 4
sriram-lab / emt-cobra
Modeling the metabolic changes during the epithelial-to-mesenchymal transition.
constraint-based-modeling omics-data-integration bioinformatics
Language:HTML 4
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.
tutorial reconstruction transcriptomics metabolic-models omics-data-integration genome-scale-models cobratoolbox
Language:MATLAB 3
esauta / TBN_learning
TBN_learning is a MATLAB implemented hybrid algorithm for learning the structure of transcriptional Bayesian networks on a genome-wide scale.
hybrid-structure-learning-algorithm bayesian-transcriptional-network omics-data-integration network-modelling network-biology
Language:MATLAB 3
selbouhaddani / PO2PLS
Probabilistic O2PLS
latent-variable-models omics omics-data-integration partial-least-squares global-test
Language:R 3
akatrib / sys-bio
Curated list of analysis pipelines for biological & clinical interpretation of data-driven findings
systems-biology bioinformatics enrichment-analysis network-analysis biomedical-data-science pathway-analysis protein-protein-interaction co-expression omics-data-integration pathway-enrichment-analysis bioinformatics-pipeline
Language:R 2
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.
microbiome-analysis omics-data-integration preprocessing
Language:Python 2
RDA-MOMSI / Dashboard
MOMSI Standard Landscape Review Curation Workflow & Multi-Omics Dashboard
genomics lipidomics metabolomics proteomics curation mass-spectrometry multiomics-data sequencing standards omics-data-integration bioimaging
Language:JavaScript 2
sriram-lab / metabolicmodeling
Constraint-based metabolic modeling software from the Chandrasekaran Lab
constraint-based-modeling genome-scale-modeling matlab python omics-data-integration fluxomics
Language:HTML 2
adityamahadevaniyer / ChIP-SICAP
Analysis of proteomics datasets obtained from ChIP-SICAP experiments in HEK cells
omics-data-integration proteomics proteomics-data-analysis rnaseq
1
annkamsk / mvae
Multimodal Variational Autoencoder dedicated to omics data integration
bioinformatics multimodal-deep-learning omics-data-integration pytorch spatial-omics
Language:Jupyter Notebook 1
crhisto / DecoFlex
DecoFlex deconvolution method for Omic data implemented as DecoFlexR
bulk-rna-seq deconvolution epigenetics methylation nmf-decomposition omics-data-integration single-cell-rna-seq
Language:R 1
ferdinand-popp / Deepan
Cluster patient based on their multiomics data utilizing graph autoencoders
graph deep learning patient omics omics-data-integration
Language:Python 1
mbongaerts / Reafect
metabolomics omics-data-integration cadd gene-prioritization kegg-pathway
Language:Jupyter Notebook 1
MendenLab / miRNAInt_Ferroptosis
Multi-omics differential expression and integration using PPI networks
differential-expression-analysis multiomics omics-data-integration protein-protein-interaction-network
Language:R 1
MetExplore / dexom-python
diversity-based enumeration of optimal context-specific metabolic networks using the cobrapy library
cobrapy constraint-based-modeling metabolism omics-data-integration optimization python
Language:Python 1
Multiomics-Analytics-Group / acore
Functionality to preprocess and analyse multi-omics data
analysis omics omics-data-integration preprocessing-data
Language:Python 1
ngiangre / ROMOPOmics
R package to parse datasets into SQLite-friendly tables
bioinformatics clinical-data omics-data-integration omop-cdm workflow
Language:R 1
NhanNguyen000 / RegOmics
This repository is the code source for the RegOmics tool - Regulatory extraction for Omics data.
bioinformatics-tool omics omics-data-integration transcriptional-regulatory-network
Language:R 1
NIB-SI / multiOmics-integration
Potato ‘omics data analysis pipelines
feature-selection network-analysis omics omics-data-integration phenotyping proteomics-data-analysis statistical-analysis
Language:HTML 1
sbl-sdsc / mcp-genelab
A Model Context Protocol (MCP) server for querying Neo4j Graph Databases with customized tools to query the NASA GeneLab Knowledge Graph
genelab mcp nasa omics omics-data-integration proto-okn spaceflight
Language:Python 1
ocbe-uio / GPTCM
Generalized promotion time cure model
bayesian-inference cell-populations multiscale-data omics-data-integration survival-analysis tumor-heterogeneity tumor-microenvironment variable-selection
Language:C++