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    37 repositories

    • metapro-data-vis

      Public
      Visualization tool for metapro
      Jupyter Notebook
      •1•1•0•0•Updated Apr 26, 2026Apr 26, 2026

    • ChickenGIT_modeling

      Public
      Code and data associated with the publication 'Multi-compartment spatiotemporal metabolic modeling of the chicken gut guides dietary intervention design'
      R
      •0•0•0•0•Updated Apr 17, 2026Apr 17, 2026

    • Ngo_WGS

      Public
      Repository for scripts associated with https://doi.org/10.1101/2025.02.28.640638
      R
      •0•0•0•0•Updated Feb 11, 2026Feb 11, 2026

    • PopNet

      Public
      Python
      •2•3•0•0•Updated Dec 15, 2025Dec 15, 2025

    • MetaPro

      Public
      Python
      •
      GNU General Public License v3.0
      •6•22•5•0•Updated Nov 12, 2025Nov 12, 2025

    • quackers

      Public
      Parkinson Lab's MG pipeline prototype
      Python
      •0•1•2•0•Updated Jul 28, 2025Jul 28, 2025

    • seq_cleaner

      Public
      Repo for a simple sequence cleaner. Removes host data, and filters for low-quality reads
      Python
      •0•0•0•0•Updated Jun 26, 2025Jun 26, 2025

    • taxa_tree_maker

      Public
      Python
      •0•0•0•0•Updated Jun 24, 2025Jun 24, 2025

    • Chicken_microbiome

      Public
      Repository for Chicken Microbiome project
      R
      •0•1•0•0•Updated May 20, 2025May 20, 2025

    • GRACE_v3

      Public
      Repository for WGS analysis of Candida albicans mutants
      Shell
      •0•0•0•0•Updated May 2, 2025May 2, 2025

    • PPI-Analysis

      Public
      Jupyter Notebook
      •0•0•0•0•Updated Apr 11, 2025Apr 11, 2025

    • bacarena_docker

      Public
      stash for bacarena docker build/install for version-lock/distribution among lab.
      Dockerfile
      •0•0•0•0•Updated Nov 4, 2024Nov 4, 2024

    • 16S_MGX_Workshops

      Public
      1•0•0•0•Updated Oct 26, 2024Oct 26, 2024

    • HiTaxon

      Public
      A hierarchical ensemble framework for taxonomic classification of short reads
      Python
      •0•2•0•0•Updated May 20, 2024May 20, 2024

    • MetaPro_tutorial

      Public
      Microbiome tutorial, running on MetaPro
      3•4•0•0•Updated May 6, 2024May 6, 2024

    • PathwayCompleteness

      Public
      Jupyter Notebook
      •0•1•0•0•Updated Apr 26, 2024Apr 26, 2024

    • cell4d

      Public
      Repository for Cell4D
      C++
      •
      Other
      •0•1•0•0•Updated Feb 13, 2024Feb 13, 2024

    • metawrap_docker

      Public
      Dockerfile
      •0•0•0•0•Updated Jan 10, 2024Jan 10, 2024

    • DeSeq2_docker

      Public
      Docker container for DeSeq2
      Dockerfile
      •0•0•0•0•Updated Jan 2, 2024Jan 2, 2024

    • Running-RGI-on-SciNet

      Public
      Running RGI tool on MetaPro outputs on SciNet
      0•0•0•0•Updated Nov 8, 2023Nov 8, 2023

    • Metatranscriptome-Workshop

      Public
      Metatranscriptomics Tutorial
      25•67•11•0•Updated Jul 3, 2023Jul 3, 2023

    • Architect

      Public
      Pipeline for automatic metabolic model reconstruction using an ensemble method for enzyme annotation
      Python
      •
      GNU General Public License v3.0
      •0•6•2•0•Updated Jun 5, 2023Jun 5, 2023

    • eps_biofilms

      Public
      HMM Models Generated from EPS Operon Prediction Project.
      bacterial-operonshmms
      bacterial-operonshmms
      Perl
      •0•1•0•0•Updated Mar 7, 2023Mar 7, 2023

    • metabolic-modeling-tools

      Public
      1•0•0•1•Updated Mar 2, 2023Mar 2, 2023

    • ToxoNet

      Public
      Repository for ToxoNet tool
      C
      •0•1•0•0•Updated Dec 1, 2022Dec 1, 2022

    • 16S_rRNA_analysis_tutorials

      Public
      The tutorials under this repository will take you through workflows for processing and analyzing 16S rRNA data.
      0•0•0•0•Updated Nov 11, 2022Nov 11, 2022

    • DETECT-v2

      Public
      Version 2 of the Density Estimation Tool for Enzyme ClassificaTion: scripts for enzyme annotation and pipeline for making the DETECT database
      Python
      •
      Other
      •3•4•0•0•Updated Jun 30, 2022Jun 30, 2022

    • Tritrichomonas-murine-microbiome-interactions

      Public
      A project interrogating the activities of murine gut protozoan Tritrichomonas, and its impact on the bacterial communities in healthy and IgA-deficient hosts. T…
      MIT License
      •1•0•0•0•Updated Apr 11, 2022Apr 11, 2022

    • gut-eukaryotes-malnutrition-and-micronutrient-supplementation

      Public
      Collection of codes used in the analysis of 16S and 18S rRNA sequencing surveys, which were conducted on stool DNA from healthy and malnourished children from P…
      R
      •
      GNU General Public License v3.0
      •1•0•0•0•Updated Oct 27, 2021Oct 27, 2021

    • Eukaryotic_microbiome_analysis

      Public
      R
      •
      GNU General Public License v3.0
      •5•0•0•0•Updated Mar 31, 2021Mar 31, 2021
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