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    15 repositories

    • MentaLiST

      Public
      The MLST pipeline developed by the PathOGiST research group
      Julia
      •
      MIT License
      •11•36•39•2•Updated Nov 29, 2023Nov 29, 2023

    • BenchmarkDR

      Public
      This is a repository for the code related to benchmarking the drug resistance prediction approaches
      Python
      •0•2•0•1•Updated Aug 4, 2022Aug 4, 2022

    • FK

      Public
      This is Nafiseh's implementation of the Fredman-Khachiyan algorithm with multiple clauses per iteration
      MATLAB
      •0•2•0•0•Updated Jun 28, 2022Jun 28, 2022

    • SplitStrains

      Public
      Jupyter Notebook
      •3•4•5•8•Updated Oct 11, 2021Oct 11, 2021

    • MongooseGUI3

      Public
      Python
      •2•0•0•0•Updated Sep 21, 2021Sep 21, 2021

    • GroupTesting

      Public
      This is a repository where we keep the code and the results of our experiments on group testing via CS
      Python
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Aug 27, 2021Aug 27, 2021

    • PathOGiST

      Public
      This repository contains the pipeline for the multi-criterion genomic analysis of bacterial pathogens
      Python
      •
      GNU General Public License v3.0
      •1•0•8•0•Updated May 15, 2020May 15, 2020

    • PythonPRINCE

      Public
      This repository contains the code for the paper "PRINCE: A Machiavellian Approach for Tandem Repeat Copy Number Approximation"
      Jupyter Notebook
      •
      MIT License
      •2•0•0•0•Updated Jan 15, 2020Jan 15, 2020

    • RFDistributionR

      Public
      The R code for computing the distribution of RF distances from a given input tree
      R
      •2•0•0•0•Updated Nov 9, 2019Nov 9, 2019

    • MLST

      Public
      Python
      •0•0•0•0•Updated Oct 19, 2019Oct 19, 2019

    • RFDistribution

      Public
      This code implements an improved version of the RF distribution computation by Bryant et al.
      Python
      •1•0•0•0•Updated Aug 28, 2019Aug 28, 2019

    • TreeShapeStats

      Public
      R
      •1•1•0•0•Updated May 26, 2019May 26, 2019

    • NGSweep

      Public
      Matthew's pipeline for preprocessing NGS data
      Python
      •
      GNU General Public License v3.0
      •0•0•3•0•Updated Nov 27, 2018Nov 27, 2018

    • RuleTB

      Public
      This repository contains the code for RuleTB, a predictor of TB lineages, from the IGE paper by Thain et al.
      R
      •0•0•0•0•Updated Aug 12, 2018Aug 12, 2018

    • Borrelia

      Public
      R
      •0•0•0•0•Updated Nov 6, 2017Nov 6, 2017