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    72 repositories

    • birdman-analyses

      Public
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •2•6•0•0•Updated Jun 9, 2026Jun 9, 2026

    • Acne_Longitudinal_Microbiome

      Public
      GitHub Repository for CMI and L'Oreal's Longitudinal Study of Acne
      Jupyter Notebook
      •0•0•0•0•Updated Apr 23, 2026Apr 23, 2026

    • haddad_apoe_fxr_KO_abs_quant

      Public
      The Github Repository for Dr. Gaby Haddad's mouse model experiment using Apoe KO and ApoeFXR KO mice under OSA-like conditions (IHC) using absolute abundance sh…
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•0•Updated Mar 21, 2026Mar 21, 2026

    • KittyBiome_reanalysis

      Public
      reanalysis of the KittyBiome dataset (collaboration with AnimalBiome)
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •1•0•0•0•Updated Oct 22, 2025Oct 22, 2025

    • gates_sepsis_bangladesh

      Public
      Metagenomic Multi-Bodysite Dataset, in collaboration with SickKids, funded by the Gates Foundation
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •1•0•0•0•Updated Sep 16, 2025Sep 16, 2025

    • OSAstudy_16S_HFHC

      Public
      Analysis of the 16S rRNA (V4) amplicon sequencing data of a mouse model (ApoE-/-) of obstructive sleep apnea on high fat, high cholesterol diet (HFHC) in collab…
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•0•Updated Apr 1, 2025Apr 1, 2025

    • U19_3xtg_5xfad_mouse_models

      Public
      3xtg and 5xfad mouse models of Alzheimer's Disease for the U19 grant
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•0•Updated Mar 18, 2025Mar 18, 2025

    • dynamics

      Public
      Analysis of Multiple Circadian/Longitudinal Datasets
      time-seriestime-series-analysismicrobiome-analysis
      time-seriestime-series-analysismicrobiome-analysismetabolome
      Jupyter Notebook
      •
      BSD 2-Clause "Simplified" License
      •0•0•0•0•Updated Aug 31, 2024Aug 31, 2024

    • marmoset-diet-change

      Public
      Shotgun metagenomic analysis of laboratory-house common marmoset breeding colony that switched from pelleted to gel diet
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•0•Updated Jan 17, 2024Jan 17, 2024

    • uc-severity-multiomics

      Public
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •5•7•3•0•Updated Jul 25, 2023Jul 25, 2023

    • greengenes2

      Public
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•3•0•0•Updated May 1, 2023May 1, 2023

    • imsms-ml

      Public
      Data exploration and analysis scripts for the machine learning analysis of the iMSMS collaboration.
      Python
      •0•2•0•0•Updated Mar 16, 2023Mar 16, 2023

    • mycobiome

      Public
      Pan-cancer mycobiome atlas
      mltcgamicrobiome
      mltcgamicrobiomemycobiome
      Jupyter Notebook
      •
      Other
      •18•33•0•0•Updated Oct 7, 2022Oct 7, 2022

    • evident-analyses

      Public
      Jupyter Notebook
      •1•2•0•0•Updated Jul 11, 2022Jul 11, 2022

    • version-testing-fastp-minimap2

      Public
      version-testing for fastp-minimap2
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •3•0•0•0•Updated Apr 15, 2022Apr 15, 2022

    • unifrac-colab-notebooks

      Public
      Notebooks for use on Google Colabs
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •1•0•0•0•Updated Apr 1, 2022Apr 1, 2022

    • mfpca-analyses

      Public
      code of simulations and real data applications for MFPCA manuscript
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •2•1•0•0•Updated Jan 3, 2022Jan 3, 2022

    • bloom-analyses

      Public
      Jupyter Notebook
      •10•2•0•0•Updated Nov 16, 2021Nov 16, 2021

    • umap-microbiome-benchmarking

      Public
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •0•2•0•0•Updated Oct 28, 2021Oct 28, 2021

    • regression-benchmarking

      Public
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •4•0•2•1•Updated Aug 5, 2021Aug 5, 2021

    • seeding-study

      Public
      Restoration of the microbiome trajectory by vaginal seeding of C-section born infants
      Jupyter Notebook
      •3•0•0•0•Updated Jun 17, 2021Jun 17, 2021

    • circadian-ihc

      Public
      Circadian Experiments - Microbiome, Metabolome
      metabolomicsmicrobiome-analysiscircadian-rhythm
      metabolomicsmicrobiome-analysiscircadian-rhythm
      Jupyter Notebook
      •
      BSD 2-Clause "Simplified" License
      •0•2•0•0•Updated Jun 2, 2021Jun 2, 2021

    • stability-analyses

      Public
      code for simulation studies and experimental microbiome data applications in Stability manuscript
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •2•1•0•0•Updated May 17, 2021May 17, 2021

    • faiths-pd-benchmarking

      Public
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •1•2•0•0•Updated May 13, 2021May 13, 2021

    • CR-2021

      Public
      Python
      •0•1•3•0•Updated Apr 18, 2021Apr 18, 2021

    • empress-analyses

      Public
      Analyses, figures, and artifacts for Empress.
      Jupyter Notebook
      •
      BSD 2-Clause "Simplified" License
      •5•1•1•1•Updated Feb 10, 2021Feb 10, 2021

    • Saliva_quantification_study

      Public
      Jupyter Notebook
      •1•0•0•0•Updated Jan 15, 2021Jan 15, 2021

    • SAF-PP-JPL

      Public
      16S analysis for assessment of the NASA Standard Spore Assay in Predicting Bacterial Populations of a Mars Mission Assembly Facility
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•0•Updated Dec 13, 2020Dec 13, 2020

    • BayesTime-analyses

      Public
      analysis code for BayeTime manuscript on simulations and microbiome applications
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •1•2•0•0•Updated Nov 12, 2020Nov 12, 2020

    • stein-schizophrenia

      Public
      BSD 2-Clause "Simplified" License
      •0•0•0•0•Updated Oct 29, 2020Oct 29, 2020
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