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    85 repositories

    • Bacterial_TRN_Dominance_and_Independence

      Public
      Repository for manuscript 'Dominance and Independence within Bacterial Transcriptional Regulation'
      Jupyter Notebook
      •
      MIT License
      •0•1•0•0•Updated Feb 20, 2026Feb 20, 2026

    • iModulonMiner_2.0

      Public
      The Repository for iModulonMiner 2.0 Manuscript
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Feb 19, 2026Feb 19, 2026

    • StressME-DynamicME

      Public
      run simulations from terminal + input files, w/visualization tools
      Jupyter Notebook
      •1•0•0•0•Updated Feb 2, 2026Feb 2, 2026

    • pymodulon

      Public
      Python package for analyzing and visualizing iModulons
      Python
      •
      MIT License
      •14•14•10•3•Updated Jan 19, 2026Jan 19, 2026

    • Pseudomonas_putida_GEMs

      Public
      Analysis of P. putida pan GEMs
      Jupyter Notebook
      •0•0•0•0•Updated Oct 17, 2025Oct 17, 2025

    • cobrame-webapp-feedback

      Public
      Issue tracking and planning for the COBRA Metabolism and Expression Modeling Web Application
      MIT License
      •0•0•0•0•Updated Oct 10, 2025Oct 10, 2025

    • PMkbase

      Public
      All code files for PMkbase.com
      HTML
      •1•0•0•0•Updated Oct 8, 2025Oct 8, 2025

    • yarrowia_lipolytica_ICA

      Public
      iModulon analysis of Y. lipolytica transcriptomes from DTU Biosustain
      Jupyter Notebook
      •0•0•0•0•Updated 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
      •4•2•6•4•Updated Aug 7, 2025Aug 7, 2025

    • modulome_pst

      Public
      iModulon structure of Pseudomonas syringae pv. tomato DC3000
      HTML
      •
      MIT License
      •0•0•0•0•Updated Jun 18, 2025Jun 18, 2025

    • GDS-Public

      Public
      Jupyter Notebook
      •
      MIT License
      •1•0•0•0•Updated Jun 11, 2025Jun 11, 2025

    • dbgwas-network

      Public
      Python
      •
      MIT License
      •0•0•0•0•Updated Apr 26, 2025Apr 26, 2025

    • ChIPdb

      Public
      A Chromatin ImmunoPrecipitation database for PROkaryotic organisms.
      HTML
      •
      MIT License
      •2•4•1•1•Updated Apr 21, 2025Apr 21, 2025

    • PromoterModeling

      Public
      Sequence-based ML models of gene regulation
      Jupyter Notebook
      •
      MIT License
      •0•3•0•0•Updated Feb 8, 2025Feb 8, 2025

    • iModulonMiner

      Public
      Workflow to download, process, and explore microbial RNA-seq data from NCBI SRA
      HTML
      •
      MIT License
      •27•27•4•3•Updated Nov 7, 2024Nov 7, 2024

    • PM_Activity_Calls

      Public
      Python notebook workflow to make metabolic activity calls on PM samples
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Sep 18, 2024Sep 18, 2024

    • ElectricColi

      Public
      Modeling and data analysis code for the E. coli extracellular electron transfer project
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Jun 29, 2024Jun 29, 2024

    • noncoding_alleleome

      Public
      Jupyter Notebook
      •
      MIT License
      •0•2•0•0•Updated 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.
      pythondockerangularbioinformaticsbig-datahelmknowledge-graphscientific-computing
      Python
      •
      Other
      •4•21•0•28•Updated 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
      •1•4•0•0•Updated Oct 19, 2023Oct 19, 2023

    • precise1k-analyze

      Public
      Jupyter Notebook
      •
      MIT License
      •1•1•0•0•Updated Oct 10, 2023Oct 10, 2023

    • modulytics

      Public
      Visualization website for the modulome, a cross-species modularization of bacterial transcriptomes
      MIT License
      •4•2•2•1•Updated Sep 16, 2023Sep 16, 2023

    • precise1k

      Public
      Jupyter Notebook
      •
      MIT License
      •0•6•1•0•Updated Aug 29, 2023Aug 29, 2023

    • IM-ML

      Public
      Jupyter Notebook
      •1•2•0•0•Updated Jul 11, 2023Jul 11, 2023

    • lifelike-website

      Public
      Lifelike landing website
      TypeScript
      •0•0•0•10•Updated May 26, 2023May 26, 2023

    • lifelike-fix-modified-date

      Public
      Python
      •0•0•0•4•Updated Mar 6, 2023Mar 6, 2023

    • Ecoli_chem_tol_ALE

      Public
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated 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
      •0•0•0•0•Updated Dec 16, 2022Dec 16, 2022

    • MASSpy

      Public
      Python
      •
      MIT License
      •7•26•10•0•Updated Dec 9, 2022Dec 9, 2022

    • soplex_cython

      Public
      Cython bindings to soplex 3.1.1
      Python
      •3•1•1•1•Updated Nov 15, 2022Nov 15, 2022