omics-data-integration

There are 2 repositories under omics-data-integration topic.

• opencobra / cobratoolbox

  The COnstraint-Based Reconstruction and Analysis Toolbox. Documentation:

  cobra-toolboxreconstructiontutorialmetabolic-modelsmetabolic-reconstructionmetabolic-engineeringgap-fillingstrain-engineeringomics-data-integrationmetabolomicstranscriptomicscobraconstraint-based-modelinghuman-metabolismmicrobiome-analysis
  Language:MATLAB 238

• BioSystemsUM / MEWpy

  Metabolic Engineering Workbench

  strainoptimizationkinetic-modelingmicrobial-communitiesmodelingomics-data-integrationpythonsimulation
  Language:Python 35

• cafferychen777 / MicrobiomeStat

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

  16s-rrnaamplicon-sequencingdada2longitudinal-datametagenomesmetagenomic-analysismicrobiomemicrobiome-analysismicrobiome-dataphyloseqqiime2statisticsvisualizationmicrobiome-workflowomicsomics-data-integration
  Language:R 24

• 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"

  binder-readyintegrative-omicsmulti-omicsomicsomics-data-integrationpapers-with-code
  Language:Jupyter Notebook 24

• 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

  microbiomemetabolomebioinformaticsomics-data-integration
  Language:Python 20

• futianfan / GenoCraft

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

  bulk-rna-seqgenomicsnext-generation-sequencingngsomicsomics-data-integrationpathway-analysisproteinrna-seqsingle-cellvisualization
  Language:SCSS 13

• pcastellanoescuder / POMA

  :package: Tools for Omics Data Analysis

  bioconductorbioinformaticsdata-visualizationdimension-reductionexploratory-data-analysismachine-learningomics-data-integrationpipelinepre-processingrr-packagerstatsstatistical-analysisuser-friendlyworkflow
  Language:R 10

• SysBioChalmers / Yarrowia_lipolytica_W29-GEM

  Genome-scale model of Yarrowia lipolytica.

  yarrowia-lipolyticametabolic-engineeringmetabolic-reconstructionsystems-biologystoichiometric-reactionsomics-data-integrationconstraint-based-modelingmetabolic-modelsmetabolic-networkgenome-scale-models
  Language:MATLAB 8

• MetExplore / dexom

  Diversity-based enumeration of optimal context-specific metabolic networks

  metabolic-networkmetabolic-reconstructionmetabolic-engineeringmetabolic-pathwaysmetabolismconstraint-based-modelingoptimizationcobra-toolboxomics-data-integration
  Language:MATLAB 5

• babessell1 / MADRID

  Metabolic Drug Repurposing Pipeline

  metabolismomics-dataomics-data-integrationconstraint-based-modelingtranscriptomicsproteomicspipelinedrug-repurposingdrug-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 ]

  bioinformaticsbiological-networksgwasomics-data-integrationpopulation-geneticsprotein-protein-interaction-networkqtl-mappingsystems-biologyyeastgene-interaction-network
  Language:Jupyter Notebook 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.

  tutorialreconstructiontranscriptomicsmetabolic-modelsomics-data-integrationgenome-scale-modelscobratoolbox
  Language:MATLAB 3

• 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.

  16s16s-rrna16s-seqanalysisdata-analysismetagenomesmetagenomic-analysismetagenomic-pipelinemetagenomicsmicrobiomemicrobiome-analysismicrobiome-analysis-pipelinesmicrobiome-datamicrobiome-workflowomicsomics-dataomics-data-analysisomics-data-integrationvisualization
  3

• akatrib / sys-bio

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

  systems-biologybioinformaticsenrichment-analysisnetwork-analysisbiomedical-data-sciencepathway-analysisprotein-protein-interactionco-expressionomics-data-integrationpathway-enrichment-analysisbioinformatics-pipeline
  Language:R 2

• 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-algorithmbayesian-transcriptional-networkomics-data-integrationnetwork-modellingnetwork-biology
  Language:MATLAB 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-analysisomics-data-integrationpreprocessing
  Language:Python 2

• selbouhaddani / PO2PLS

  Probabilistic O2PLS

  latent-variable-modelsomicsomics-data-integrationpartial-least-squaresglobal-test
  Language:R 2

• sriram-lab / emt-cobra

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

  constraint-based-modelingomics-data-integrationbioinformatics
  Language:HTML 2

• sriram-lab / metabolicmodeling

  Constraint-based metabolic modeling software from the Chandrasekaran Lab

  constraint-based-modelinggenome-scale-modelingmatlabpythonomics-data-integrationfluxomics
  Language:HTML 2

• adityamahadevaniyer / ChIP-SICAP

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

  proteomics-data-analysisproteomicsrnaseqomics-data-integration
  1

• annkamsk / mvae

  Multimodal Variational Autoencoder dedicated to omics data integration

  bioinformaticsmultimodal-deep-learningomics-data-integrationpytorchspatial-omics
  Language:Jupyter Notebook 1

• crhisto / DecoFlex

  DecoFlex deconvolution method for Omic data implemented as DecoFlexR

  bulk-rna-seqdeconvolutionepigeneticsmethylationnmf-decompositionomics-data-integrationsingle-cell-rna-seq
  Language:R 1

• ferdinand-popp / Deepan

  Cluster patient based on their multiomics data utilizing graph autoencoders

  graphdeeplearningpatientomicsomics-data-integration
  Language:Python 1

• mbongaerts / Reafect

  caddgene-prioritizationkegg-pathwaymetabolomicsomics-data-integration
  Language:Jupyter Notebook 1

• MendenLab / miRNAInt_Ferroptosis

  Multi-omics differential expression and integration using PPI networks

  differential-expression-analysismultiomicsomics-data-integrationprotein-protein-interaction-network
  Language:R 1

• MetExplore / dexom-python

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

  cobrapyconstraint-based-modelingmetabolismomics-data-integrationoptimizationpython
  Language:Python 1

• ngiangre / ROMOPOmics

  R package to parse datasets into SQLite-friendly tables

  omop-cdmbioinformaticsclinical-dataomics-data-integrationworkflow
  Language:R 1

• NhanNguyen000 / RegOmics

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

  bioinformatics-toolomicsomics-data-integrationtranscriptional-regulatory-network
  Language:R 1

• shashank-KU / OmniCorr

  Calculate correlation between two omics data

  correlationdata-visualizationromics-data-integration
  Language:R 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.

  autoimmune-diseaseimmunogenomicsomics-data-integrationsingle-cellr
  Language:Jupyter Notebook 0

• nara3m / nara3m

  Nara Marella

  cheminformaticsdata-sciencedatabasesgdprlaboratory-information-management-systemlipidomicsmetabolomicsomics-data-integrationproteomicsresearch-data-managementtranscriptomics
  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.

  bioinformaticsmulti-omic-integrationomicsomics-data-integrationr-programmingtranscriptomics
  Language:R 0

• ScottCampit / single-cell-neutrophil-flux-analysis

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

  cobraflux-balance-analysisimmune-systemmatlabomics-data-integrationpublication-codepythonrprogrammingsingle-cell-analysissingle-cell-rna-seq
  Language:HTML 0

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

  data analytics & machine learning meet genetics @ AUC

  genomicsbioinformaticssystems-biologyomicsomics-data-integrationmachine-learning
  Language:JavaScript 0

• ikmb / OmLiT

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

  omics-data-integrationhlaimmunoinformaticsrust-bindingsbioinformaticsdata-preprocessingdata-preparation
  Language:Rust

• ocbe-uio / BayesSurvive

  Bayesian survival models for high-dimensional data

  bayesian-cox-modelsbayesian-variable-selectiongraph-learningomics-data-integrationsurvival-analysishigh-dimensional-statistics
  Language:R