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@microbial-pangenomes-lab Microbial Pangenomes Lab

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    15 repositories

    • microbial-pangenomes-lab.github.io

      Public
      HTML
      •
      MIT License
      •0•0•0•0•Updated Oct 22, 2024Oct 22, 2024

    • microGWAS

      Public template
      Bacterial GWAS analysis
      Python
      •
      MIT License
      •1•31•4•0•Updated Sep 26, 2024Sep 26, 2024

    • panfeed

      Public
      A k-mer counter that streams gene-cluster specific k-mers, while keeping k-mer positional information. Useful for microbial GWAS analyses with higher interpretability.
      gwask-mer-countingk-mers
      Python
      •
      Apache License 2.0
      •0•8•0•0•Updated Sep 2, 2024Sep 2, 2024

    • bacterial_transcription

      Public
      Python
      •0•0•0•0•Updated Aug 30, 2024Aug 30, 2024

    • 2022_sarscov2_epistasis

      Public
      Estimating epistatic interactions from SARS-CoV-2 genomes
      Jupyter Notebook
      •
      MIT License
      •1•1•0•0•Updated Jul 12, 2024Jul 12, 2024

    • plate_reader_evolution

      Public
      Evolution experiments in microplate formats
      Python
      •
      MIT License
      •0•0•0•0•Updated Jul 1, 2024Jul 1, 2024

    • ChiBio

      Public
      ChiBio primary operating system.
      Python
      •30•0•0•0•Updated May 31, 2024May 31, 2024

    • 2023_ecoli_protection

      Public
      Python
      •
      MIT License
      •0•1•0•0•Updated Feb 13, 2024Feb 13, 2024

    • panaroo

      Public
      An updated pipeline for pangenome investigation
      Python
      •
      MIT License
      •33•0•0•0•Updated Dec 7, 2023Dec 7, 2023

    • SalisLabCode

      Public
      Models, design algorithms, and other software related to Salis lab publications
      Python
      •20•0•0•0•Updated Aug 21, 2023Aug 21, 2023

    • panfeed_benchmark_scripts

      Public
      This repository contains the scripts that were used to test panfeed and visualize results of other programs.
      Python
      •
      MIT License
      •0•0•0•0•Updated Mar 7, 2023Mar 7, 2023

    • CodeClub_Rosalind

      Public
      MIT License
      •0•0•0•0•Updated May 19, 2022May 19, 2022

    • 2022_python_course

      Public
      Introduction to python for biologists (2022 edition)
      Jupyter Notebook
      •
      Apache License 2.0
      •0•0•0•0•Updated Mar 24, 2022Mar 24, 2022

    • 2021_ecoli_pathogenicity

      Public
      Bacterial GWAS for E. coli BSI genetic determinants
      Jupyter Notebook
      •
      MIT License
      •1•1•0•0•Updated Feb 15, 2022Feb 15, 2022

    • BacGWASim

      Public
      A Simulator for Bacterial Machine learning and Genome-Wide Association Studies
      Python
      •
      MIT License
      •5•1•0•0•Updated Aug 17, 2021Aug 17, 2021