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  1. lorepy Public

    A library to create lore plots (logistic regression of the prevalence of a categorical variable in function of a continuous feature)

    Python 16 2

  2. covid19_respiratory_microbiome Public

    Code accompanying the manuscript "Clinical practices underlie COVID-19 patient respiratory microbiome composition and its interactions with the host"

    R 4 3

  3. benchmark_microbiome_transformations Public

    Forked from vllorens/benchmark_microbiome_transformations

    Code to reproduce the analyses from the paper "Benchmarking microbiome transformations favors experimental quantitative approaches to address compositionality and sampling depth biases"

    R 8 1

  4. omixer-rpm Public

    A Reference Pathways Mapper for turning metagenomic functional profiles into pathway/module profiles.

    Java 26 8

  5. GMMs Public

    A manually curated database of human gut metabolic modules.

    17 5

  6. QMP Public

    Quantitative Microbiome Profiling

    R 15 8

Repositories

Showing 10 of 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 0 0 0 0 Updated Jan 15, 2025
  • lorepy Public

    A library to create lore plots (logistic regression of the prevalence of a categorical variable in function of a continuous feature)

    Python 16 2 3 0 Updated Jan 10, 2025
  • loreplotr Public

    Logistic regression plots in R

    R 1 1 3 (1 issue needs help) 0 Updated Jan 9, 2025
  • dyspyosis Public

    A python package to calculate the dysbiosis score in microbiome datasets

    Python 1 1 1 0 Updated Jan 1, 2025
  • prodiphy Public
    Python 0 0 0 0 Updated Nov 12, 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 5 MIT 0 0 0 Updated Jul 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).

    0 0 0 0 Updated Jun 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.

    0 0 0 0 Updated Jun 21, 2024
  • mocat2 Public Forked from mocat2/mocat2

    Latest MOCAT2 version

    Perl 0 GPL-3.0 14 0 0 Updated May 30, 2024
  • RLdbRDA Public

    The RaesLab's implementation of a distance based Redundancy Analysis (dbRDA)

    R 4 1 3 (1 issue needs help) 0 Updated Mar 6, 2024