Skip to content
Change the repository type filter

All

    Repositories list

    • Repository for manuscript 'Dominance and Independence within Bacterial Transcriptional Regulation'
      Jupyter Notebook
      MIT License
      0100Updated Dec 11, 2024Dec 11, 2024
    • Sequence-based ML models of gene regulation
      Jupyter Notebook
      MIT License
      1100Updated Dec 1, 2024Dec 1, 2024
    • Workflow to download, process, and explore microbial RNA-seq data from NCBI SRA
      HTML
      MIT License
      23831Updated Nov 7, 2024Nov 7, 2024
    • pymodulon

      Public
      Python package for analyzing and visualizing iModulons
      Python
      MIT License
      141183Updated Oct 28, 2024Oct 28, 2024
    • pyphylon

      Public
      Python package for analyzing and visualizing co-occuring gene / allele sets (phylons) within a pangenome
      Python
      MIT License
      0170Updated Sep 27, 2024Sep 27, 2024
    • Python notebook workflow to make metabolic activity calls on PM samples
      Jupyter Notebook
      MIT License
      0000Updated Sep 18, 2024Sep 18, 2024
    • PMkbase

      Public
      All code files for PMkbase.com
      HTML
      MIT License
      0000Updated Aug 30, 2024Aug 30, 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
      0000Updated May 8, 2024May 8, 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
      420028Updated 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
      0000Updated Oct 10, 2023Oct 10, 2023
    • Visualization website for the modulome, a cross-species modularization of bacterial transcriptomes
      MIT License
      4121Updated Sep 16, 2023Sep 16, 2023
    • precise1k

      Public
      Jupyter Notebook
      MIT License
      0410Updated Aug 29, 2023Aug 29, 2023
    • IM-ML

      Public
      Jupyter Notebook
      1100Updated Jul 11, 2023Jul 11, 2023
    • Lifelike landing website
      TypeScript
      00010Updated May 26, 2023May 26, 2023
    • iModulon structure of Pseudomonas syringae pv. tomato DC3000
      HTML
      MIT License
      0000Updated Apr 22, 2023Apr 22, 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
      62290Updated Dec 9, 2022Dec 9, 2022
    • Cython bindings to soplex 3.1.1
      Python
      3111Updated Nov 15, 2022Nov 15, 2022
    • Design oligos for RiboRid protocol
      Python
      1130Updated Nov 12, 2022Nov 12, 2022
    • precise2

      Public
      HTML
      MIT License
      5220Updated Jun 3, 2022Jun 3, 2022
    • iModulon structure of Acinetobacter baumannii AB5075
      HTML
      MIT License
      0000Updated May 30, 2022May 30, 2022
    • ME-script

      Public
      Notebooks for solving COBRAme models
      Jupyter Notebook
      0000Updated May 8, 2022May 8, 2022
    • iModulon structure of Pseudomonas putida KT2440
      HTML
      MIT License
      0300Updated Apr 28, 2022Apr 28, 2022
    • Lifelike's custom Keycloak Docker image
      CSS
      0000Updated Mar 26, 2022Mar 26, 2022
    • Python
      0000Updated Mar 8, 2022Mar 8, 2022