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@Gibbons-Lab

Gibbons Lab

The Gibbons Lab -- Microbial Systems Ecology and Evolution at the Institute for Systems Biology.

Pinned

  1. wiki wiki Public

    General good-to-know stuff.

    1

  2. manuals-and-policies manuals-and-policies Public

    2 2

  3. pipelines pipelines Public

    Pipelines used in the lab.

    Nextflow 8 2

  4. mbtools mbtools Public

    R package for microbiome analysis. Provides helper functions for common workflows ranging from preprocessing to visualization.

    R 20 9

  5. isb_course_2022 isb_course_2022 Public

    Materials and presentation for the 2022 ISB Microbiome course.

    Jupyter Notebook 24 9

  6. american-gut-app american-gut-app Public

    Source repository for the American Gut App.

    Python 1 1

Repositories

Showing 10 of 37 repositories
  • Aberrant-BMF-Cell-Reports Public

    Aberrant bowel movement frequencies coincide with increased microbe-derived blood metabolites associated with reduced organ function.

    Jupyter Notebook 1 2 0 0 Updated May 29, 2024
  • 2023_URTmetaanalysis Public
    Jupyter Notebook 0 0 0 0 Updated Apr 22, 2024
  • IBT-and-the-Gut-Microbiome Public

    Repository containing the scripts, the intermediate files, and the data used in the manuscript, "Island biogeography theory and the gut microbiome: why taller people tend to harbor more diverse gut microbiomes"

    Jupyter Notebook 0 0 0 0 Updated Apr 12, 2024
  • medi Public

    Metagenomic Estimation of Dietary Intake and Content.

    R 8 Apache-2.0 2 2 0 Updated Apr 10, 2024
  • scfa_predictions Public

    Microbial community-scale metabolic modeling predicts personalized short-chain-fatty-acid production profiles in the human gut

    Jupyter Notebook 2 0 0 0 Updated Apr 1, 2024
  • gapseq-docker Public

    A docker image for gapseq.

    Dockerfile 0 Apache-2.0 0 0 0 Updated Mar 18, 2024
  • medi-paper Public

    The accompanying paper for the MEDI method.

    0 Apache-2.0 0 0 0 Updated Feb 2, 2024
  • isb_course_2023 Public

    Materials and presentation for the 2023 ISB Microbiome course.

    Jupyter Notebook 18 Apache-2.0 10 0 0 Updated Jan 26, 2024
  • mbtools Public

    R package for microbiome analysis. Provides helper functions for common workflows ranging from preprocessing to visualization.

    R 20 Apache-2.0 9 2 0 Updated Jan 24, 2024
  • pipelines Public

    Pipelines used in the lab.

    Nextflow 8 Apache-2.0 2 0 0 Updated Jan 23, 2024
View all repositories

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