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    79 repositories

    • PromoterModeling

      Public
      Sequence-based ML models of gene regulation
      Jupyter Notebook
      •
      MIT License
      •1•1•0•0•Updated Dec 1, 2024Dec 1, 2024

    • iModulonMiner

      Public
      Workflow to download, process, and explore microbial RNA-seq data from NCBI SRA
      HTML
      •
      MIT License
      •23•7•3•1•Updated Nov 7, 2024Nov 7, 2024

    • pymodulon

      Public
      Python package for analyzing and visualizing iModulons
      Python
      •
      MIT License
      •14•11•8•3•Updated 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
      •0•1•7•0•Updated Sep 27, 2024Sep 27, 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

    • PMkbase

      Public
      All code files for PMkbase.com
      HTML
      •
      MIT License
      •0•0•0•0•Updated Aug 30, 2024Aug 30, 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

    • GDS-Public

      Public
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated May 8, 2024May 8, 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•20•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•3•0•0•Updated Oct 19, 2023Oct 19, 2023

    • precise1k-analyze

      Public
      Jupyter Notebook
      •
      MIT License
      •0•0•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•1•2•1•Updated Sep 16, 2023Sep 16, 2023

    • precise1k

      Public
      Jupyter Notebook
      •
      MIT License
      •0•4•1•0•Updated Aug 29, 2023Aug 29, 2023

    • IM-ML

      Public
      Jupyter Notebook
      •1•1•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

    • modulome_pst

      Public
      iModulon structure of Pseudomonas syringae pv. tomato DC3000
      HTML
      •
      MIT License
      •0•0•0•0•Updated Apr 22, 2023Apr 22, 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
      •6•22•9•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

    • RiboRid_Design

      Public
      Design oligos for RiboRid protocol
      Python
      •1•1•3•0•Updated Nov 12, 2022Nov 12, 2022

    • precise2

      Public
      HTML
      •
      MIT License
      •5•2•2•0•Updated Jun 3, 2022Jun 3, 2022

    • modulome_abaum

      Public
      iModulon structure of Acinetobacter baumannii AB5075
      HTML
      •
      MIT License
      •0•0•0•0•Updated May 30, 2022May 30, 2022

    • ME-script

      Public
      Notebooks for solving COBRAme models
      Jupyter Notebook
      •0•0•0•0•Updated May 8, 2022May 8, 2022

    • modulome_ppu

      Public
      iModulon structure of Pseudomonas putida KT2440
      HTML
      •
      MIT License
      •0•3•0•0•Updated Apr 28, 2022Apr 28, 2022

    • lifelike-keycloak

      Public
      Lifelike's custom Keycloak Docker image
      CSS
      •0•0•0•0•Updated Mar 26, 2022Mar 26, 2022

    • dbgwas-network

      Public
      Python
      •0•0•0•0•Updated Mar 8, 2022Mar 8, 2022

    • reference_sequences

      Public
      Internal reference sequence bank
      2•0•0•1•Updated Dec 14, 2021Dec 14, 2021