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    20 repositories

    • Webservices-tester

      Public
      A test script to check operational status of various webservices used in our questionnaires. Triggered daily using GitHub Actions.
      Python
      •
      Other
      •0•0•0•0•Updated Oct 26, 2024Oct 26, 2024

    • prodiphy

      Public
      Python
      •
      Other
      •0•0•0•0•Updated Oct 9, 2024Oct 9, 2024

    • dyspyosis

      Public
      A python package to calculate the dysbiosis score in microbiome datasets
      pythonpackagedata-sciencedeep-learningneural-networkmicrobiomemicrobiome-analysis
      Python
      •
      Other
      •1•1•1•0•Updated Oct 1, 2024Oct 1, 2024

    • lorepy

      Public
      A library to create lore plots (logistic regression of the prevalence of a categorical variable in function of a continuous feature)
      pythonpandaspython3matplotlibdatavisualization
      Python
      •
      Other
      •2•15•3•0•Updated Oct 1, 2024Oct 1, 2024

    • loreplotr

      Public
      Logistic regression plots in R
      R
      •
      Other
      •1•1•1•0•Updated Oct 1, 2024Oct 1, 2024

    • QMP-Microbiome-CRC-confounders

      Public
      Scripts for the manuscript "Microbiome confounders and quantitative profiling challenge established microbial targets in colorectal cancer developmental stages"
      HTML
      •
      MIT License
      •0•5•0•0•Updated Jul 29, 2024Jul 29, 2024

    • Tara-Oceans-Plankton-Interactome

      Public
      Supplemental data and website for Lima-Mendez, G., et al. (2015). Determinants of community structure in the global plankton interactome Science, 348(6237).
      microbiomeplanktonocean-sciences
      0•0•0•0•Updated Jun 21, 2024Jun 21, 2024

    • Tara-Oceans-Plankton-Networks

      Public
      Supplemental data and website for Guidi, L., et al. (2016). Plankton networks driving carbon export in the oligotrophic ocean, Nature.
      microbiomeplanktonocean-sciences
      0•0•0•0•Updated Jun 21, 2024Jun 21, 2024

    • mocat2

      Public
      Latest MOCAT2 version
      Perl
      •
      GNU General Public License v3.0
      •14•0•0•0•Updated May 30, 2024May 30, 2024

    • RLdbRDA

      Public
      The RaesLab's implementation of a distance based Redundancy Analysis (dbRDA)
      R
      •
      Other
      •1•4•3•0•Updated Mar 6, 2024Mar 6, 2024

    • Enterotype-prediction-based-on-the-life-history

      Public
      Machine learning classification pipe-line used for the study "Long-term life history predicts current elderly gut microbiome"
      rmicrobiologymicrobiome
      R
      •
      GNU General Public License v3.0
      •0•3•0•0•Updated Jul 19, 2022Jul 19, 2022

    • covid19_respiratory_microbiome

      Public
      Code accompanying the manuscript "Clinical practices underlie COVID-19 patient respiratory microbiome composition and its interactions with the host"
      R
      •
      GNU General Public License v3.0
      •3•4•1•0•Updated Sep 23, 2021Sep 23, 2021

    • benchmark_microbiome_transformations

      Public
      Code to reproduce the analyses from the paper "Benchmarking microbiome transformations favors experimental quantitative approaches to address compositionality and sampling depth biases"
      R
      •
      GNU General Public License v3.0
      •4•8•0•0•Updated May 5, 2021May 5, 2021

    • QMP

      Public
      Quantitative Microbiome Profiling
      R
      •
      BSD 3-Clause "New" or "Revised" License
      •8•15•1•0•Updated Mar 13, 2021Mar 13, 2021

    • temporal_variability_microbiome_qmp

      Public
      R
      •
      BSD 3-Clause "New" or "Revised" License
      •0•2•0•0•Updated Mar 9, 2021Mar 9, 2021

    • fgfp-gwas

      Public
      Replication Cookbook for FGFP GWAS
      R
      •6•0•0•0•Updated Jul 13, 2020Jul 13, 2020

    • BMIS

      Public
      R
      •0•1•0•0•Updated Nov 13, 2019Nov 13, 2019

    • omixer-rpm

      Public
      A Reference Pathways Mapper for turning metagenomic functional profiles into pathway/module profiles.
      metagenomicspathway-analysismetabolic-reconstruction
      Java
      •
      Other
      •8•26•2•0•Updated Nov 21, 2018Nov 21, 2018

    • GMMs

      Public
      A manually curated database of human gut metabolic modules.
      metagenomicspathway-analysismetabolic-reconstruction
      Other
      •5•17•1•0•Updated Jul 27, 2018Jul 27, 2018

    • raeslab-utils

      Public
      Python
      •
      GNU General Public License v3.0
      •2•4•0•0•Updated Jul 18, 2018Jul 18, 2018