Skip to content
Change the repository type filter

All

    Repositories list

    • pymodulon

      Public
      Python package for analyzing and visualizing iModulons
      Python
      MIT License
      1415103Updated Apr 27, 2026Apr 27, 2026
    • PMkbase

      Public
      All code files for PMkbase.com
      HTML
      2000Updated Apr 27, 2026Apr 27, 2026
    • Repository for manuscript 'Disentangling factors affecting bacterial transcriptional regulatory network inference'
      Jupyter Notebook
      MIT License
      0100Updated Feb 20, 2026Feb 20, 2026
    • The Repository for iModulonMiner 2.0 Manuscript
      Jupyter Notebook
      MIT License
      0000Updated Feb 19, 2026Feb 19, 2026
    • run simulations from terminal + input files, w/visualization tools
      Jupyter Notebook
      1000Updated Feb 2, 2026Feb 2, 2026
    • Analysis of P. putida pan GEMs
      Jupyter Notebook
      0000Updated Oct 17, 2025Oct 17, 2025
    • Issue tracking and planning for the COBRA Metabolism and Expression Modeling Web Application
      MIT License
      0000Updated Oct 10, 2025Oct 10, 2025
    • iModulon analysis of Y. lipolytica transcriptomes from DTU Biosustain
      Jupyter Notebook
      0000Updated Aug 19, 2025Aug 19, 2025
    • pyphylon

      Public
      Python package for analyzing and visualizing co-occuring gene / allele sets (phylons) within a pangenome
      Python
      MIT License
      3265Updated Aug 7, 2025Aug 7, 2025
    • iModulon structure of Pseudomonas syringae pv. tomato DC3000
      HTML
      MIT License
      0000Updated Jun 18, 2025Jun 18, 2025
    • Jupyter Notebook
      MIT License
      2000Updated Jun 11, 2025Jun 11, 2025
    • Python
      MIT License
      0000Updated Apr 26, 2025Apr 26, 2025
    • ChIPdb

      Public
      A Chromatin ImmunoPrecipitation database for PROkaryotic organisms.
      HTML
      MIT License
      2411Updated Apr 21, 2025Apr 21, 2025
    • Sequence-based ML models of gene regulation
      Jupyter Notebook
      MIT License
      0400Updated Feb 8, 2025Feb 8, 2025
    • Workflow to download, process, and explore microbial RNA-seq data from NCBI SRA
      HTML
      MIT License
      292943Updated Nov 7, 2024Nov 7, 2024
    • Python notebook workflow to make metabolic activity calls on PM samples
      Jupyter Notebook
      MIT License
      0000Updated Sep 18, 2024Sep 18, 2024
    • Modeling and data analysis code for the E. coli extracellular electron transfer project
      Jupyter Notebook
      MIT License
      0000Updated Jun 29, 2024Jun 29, 2024
    • Jupyter Notebook
      MIT License
      0200Updated Apr 16, 2024Apr 16, 2024
    • lifelike

      Public archive
      Turning big data into contextualized knowledge. Lifelike is a modern application platform for data extraction, analysis and visualization.
      Python
      Other
      422028Updated Apr 4, 2024Apr 4, 2024
    • MetPath

      Public
      MetPath is a set of functions for performing metabolic pathway-based gene expression analysis using genome-scale metabolic models
      MATLAB
      MIT License
      1300Updated Oct 19, 2023Oct 19, 2023
    • Jupyter Notebook
      MIT License
      1100Updated Oct 10, 2023Oct 10, 2023
    • Visualization website for the modulome, a cross-species modularization of bacterial transcriptomes
      MIT License
      4221Updated Sep 16, 2023Sep 16, 2023
    • precise1k

      Public
      Jupyter Notebook
      MIT License
      0610Updated Aug 29, 2023Aug 29, 2023
    • IM-ML

      Public
      Jupyter Notebook
      1200Updated Jul 11, 2023Jul 11, 2023
    • Lifelike landing website
      TypeScript
      00010Updated May 26, 2023May 26, 2023
    • Python
      0004Updated Mar 6, 2023Mar 6, 2023
    • Jupyter Notebook
      MIT License
      0000Updated Jan 6, 2023Jan 6, 2023
    • ROS-ALE

      Public
      Generates all figures for the manuscript "Laboratory evolution and advanced data analytics reveal systems biology of ROS tolerance" by Kevin Rychel, et al.
      Jupyter Notebook
      MIT License
      0000Updated Dec 16, 2022Dec 16, 2022
    • MASSpy

      Public
      Python
      MIT License
      726100Updated Dec 9, 2022Dec 9, 2022
    • Cython bindings to soplex 3.1.1
      Python
      3111Updated Nov 15, 2022Nov 15, 2022
    ProTip! When viewing an organization's repositories, you can use the props. filter to filter by custom property.