gut-microbiome

There are 18 repositories under gut-microbiome topic.

  • franciscozorrilla/metaGEM

    :gem: An easy-to-use workflow for generating context specific genome-scale metabolic models and predicting metabolic interactions within microbial communities directly from metagenomic data

    Language:Python204512142

  • jaeyunsung/GMHI_2020

    Scripts for reproducing results shown in Gupta VK et al. "A Predictive Index for Health Status using Species-level Gut Microbiome Profiling". Nature Communications, 2020. https://doi.org/10.1038/s41467-020-18476-8.

    Language:R312616

  • GRONINGEN-MICROBIOME-CENTRE/MicrobeRX

    MicrobeRX

    Language:Python8502

  • Wishartlab-openscience/Biotransformer

    A computational tool for the prediction and identification of metabolites.

    Language:Java6002

  • microsud/Indian-gut-microbiota

    Data and analysis code for the Indian gut microbiota study

    Language:R4201

  • erictleung/microbiome-analysis-resources

    :microscope: Resources and notes on studying the human microbiome

    323

  • gaospecial/gut-microbiome-20yrs

    Gut microbiome study (from 2000 to 2020)

    Language:HTML3400

  • GeorgeMcLellan/SCD-Food-List-Android

    An Android app to help people on the Specific Carbohydrate Diet (SCD) check if a food is allowed or not on the diet. This app is endorsed by Kirkton Press Limited, owner of the SCD trademark.

    Language:Kotlin2200

  • gntoulaveris/bioenergetic-pathways-human-gut

    Analysis and visualization of bioenergetic pathways in human gut microbiome datasets.

    Language:R2100

  • brenoslivio/GutMicrobiomeAnalysis

    Analysis and machine learning of high-dimensional data from the human gut microbiome.

    Language:Jupyter Notebook1100

  • gletroadec/Projet_5.1

    Les études de métagénomiques mettent en évidence la présence et l'absence de différentes souches dans un microbiome. Pour résumer les abondances, on peut établir des graphes de co-occurence via : Rapid inference of direct interactions in large-scale ecological networks from heterogeneous microbial sequencing data, Janko Tackmann, Joao Frederico Matias Rodrigues, Christian von Mering. bioRxiv 390195; doi : https://doi.org/10.1101/390195 Cependant, ces techniques reposent sur des corrélations et non sur des causalités. Elles ne permettent pas de comprendre les interactions entre organismes. Pour cela, il est important d'intégrer une autre dimension comme les informations contenues dans les réseaux métaboliques des bactéries. Pour cela, certaines bases de données existent : Brunk E, Sahoo S, Zielinski DC, Altunkaya A, Dräger A, Mih N, et al. Recon3D enables a three-dimensional view of gene variation in human metabolism. Nat Biotechnol. Nature Publishing Group; 2018 Mar;36(3):272-81 https://github.com/cdanielmachado/carveme/tree/master/carveme Ce projet vise à proposer une stratégie pour détecter les interactions via les échanges de métabolites via Flux Variability Analysis. La stratégie sera a tester sur des données de microbiotes intestinales fournies par le projet HMP.

    Language:Python1100

  • PulmonomicsLab/mdpd

    MDPD - Microbiome Database of Pulmonary Diseases

    Language:PHP1100

  • val92loz/HFD-NR_microbiome

    This repository provides the scripts used to analyze the metagenomics data from the paper Nicotinamide Riboside-Conditioned Microbiota Deflects High-Fat Diet-Induced Weight Gain in Mice.

    Language:Python1100

  • baijinbing/agpobesity

    agp data to understand gut microbiome and childhood obesity.

    Language:R0101

  • hghezzi/Replication_Rate_Snakemake

    Snakemake workflow to calculate in vivo bacterial replication rates from single time point metagenomics sequencing

    0101

  • iliapopov17/PNMIM

    📑Reports and bioinformatics analyses from internship in Indonesia

    Language:HTML0100

  • jajohnso29/jajohnso29

    My professional repository of project and publication data files in computational biology and data science.

    0100

  • Shuyib/mouse_gut_OTU

    Vectorization and Unsupervised Learning of Mouse Operation Taxonomic Units to determine which species of bacteria form distinct groups in a dataset.

    Language:Jupyter Notebook201