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    14 repositories

    • ICU_Analysis

      Public
      This repository contains code for a study evaluating whether gut microbiome profiles can improve prediction of infection and mortality in critically ill ICU patients. Data sourced with the help of Dr. Daniel Freedberg at CUMC
      Jupyter Notebook
      •0•0•0•0•Updated May 15, 2025May 15, 2025

    • DEBIAS-M

      Public
      Python
      •
      Other
      •0•2•0•0•Updated Apr 7, 2025Apr 7, 2025

    • RebalancedCV

      Public
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•2•0•0•Updated Mar 22, 2025Mar 22, 2025

    • LPOCV-bias-analysis

      Public
      Analysis support the manuscript "Distributional bias compromises leave-one-out cross-validation"
      Jupyter Notebook
      •0•0•0•0•Updated Mar 17, 2025Mar 17, 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

    • CopanTopologyAnalysis

      Public
      Python
      •0•0•0•0•Updated Dec 12, 2024Dec 12, 2024

    • DEBIAS-M-Analysis

      Public
      Jupyter Notebook
      •0•0•0•0•Updated Oct 18, 2024Oct 18, 2024

    • SGVFinder2

      Public
      Python
      •
      Other
      •2•7•11•1•Updated Aug 8, 2024Aug 8, 2024

    • pymgpipe

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

    • 2023_Metamobilome

      Public
      Python
      •0•0•0•0•Updated Sep 29, 2023Sep 29, 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
      •21•0•0•0•Updated Apr 13, 2020Apr 13, 2020