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    22 repositories

    • Lymphoma-Microbiome

      Public
      Analysis code files for the paper titled "The gut microbiome and mycobiome landscape of treatment-naïve lymphoma" by Zaznaev A., Mars R. et al.
      Python
      •0•0•0•0•Updated Sep 3, 2026Sep 3, 2026

    • MAG-E

      Public
      Python
      •
      Other
      •1•2•1•0•Updated Aug 25, 2026Aug 25, 2026

    • GE_cancer_microbes_reanalysis

      Public
      Code and plots supporting Supplementary Note 3 of the manuscript titled "Tumor-specific microbial signatures generalize across clinical sites, laboratories, bio…
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•0•Updated Jul 14, 2026Jul 14, 2026

    • SLICE

      Public
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•0•Updated Jul 13, 2026Jul 13, 2026

    • SLICE_analysis

      Public
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•0•Updated Jul 13, 2026Jul 13, 2026

    • MAG-E_analysis

      Public
      Code, data, and data descriptions associated with the MAG-E manuscript.
      Python
      •
      Other
      •0•0•0•0•Updated Apr 14, 2026Apr 14, 2026

    • DEBIAS-M

      Public
      Python
      •
      Other
      •1•4•0•0•Updated Mar 12, 2026Mar 12, 2026

    • MANU_copangraph

      Public
      Jupyter Notebook
      •0•0•0•0•Updated Feb 23, 2026Feb 23, 2026

    • FMF_numom2b

      Public
      Python
      •0•0•0•0•Updated Feb 22, 2026Feb 22, 2026

    • RebalancedCV

      Public
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•5•0•2•Updated Feb 17, 2026Feb 17, 2026

    • ESCC_microbiome_16S_analysis

      Public
      Results and code used to generate figures supporting "A generalizable cross-continent prediction of esophageal squamous cell carcinoma using the oral microbiome…
      Python
      •0•0•0•0•Updated Feb 3, 2026Feb 3, 2026

    • copangraph

      Public
      Comparative pan-metagenomic graph.
      Shell
      •
      Other
      •1•9•0•0•Updated Nov 27, 2025Nov 27, 2025

    • metagenome_matcher

      Public
      Python
      •
      Other
      •0•1•0•0•Updated Nov 27, 2025Nov 27, 2025

    • DEBIAS-M-Analysis

      Public
      Jupyter Notebook
      •0•0•0•0•Updated Oct 20, 2025Oct 20, 2025

    • SGVFinder2

      Public
      Python
      •
      Other
      •4•9•15•1•Updated Oct 3, 2025Oct 3, 2025

    • LPOCV-bias-analysis

      Public
      Analysis supporting the manuscript "Distributional bias compromises leave-one-out cross-validation"
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •0•1•0•0•Updated Sep 16, 2025Sep 16, 2025

    • compositional-empty-features

      Public
      Analysis of our manuscript entitled "Compositional transformations can reasonably introduce phenotype-associated values in sparse features"
      Jupyter Notebook
      •0•0•0•0•Updated Jan 6, 2025Jan 6, 2025

    • preeclampsia_analysis

      Public
      Analysis supporting the manuscript "Early prediction of preeclampsia using the first trimester vaginal microbiome"
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•0•Updated Dec 22, 2024Dec 22, 2024

    • pymgpipe

      Public
      Python implementation of mgpipe
      modelingsystems-biologymicrobiome
      modelingsystems-biologymicrobiomecobrametabolic-modelsflux-balance-analysismetabolic-reconstructionmicrobiome-modeling-toolboxmgpipe
      JetBrains MPS
      •
      Apache License 2.0
      •1•7•0•1•Updated Oct 9, 2023Oct 9, 2023

    • PTB_Metabs_2021

      Public
      Python
      •1•0•0•0•Updated Sep 11, 2023Sep 11, 2023

    • MOMs-PI_microdiversity_2023

      Public
      Jupyter Notebook
      •1•2•0•0•Updated Jul 15, 2023Jul 15, 2023

    • mantis

      Public
      Mantis: A Fast, Small, and Exact Large-Scale Sequence-Search Index
      C++
      •
      BSD 3-Clause "New" or "Revised" License
      •23•0•0•0•Updated Apr 13, 2020Apr 13, 2020
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