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    35 repositories

    • arete

      Public
      AMR/VF LGT focused bacterial genomics analysis workflow
      pipelinenextflowreproducible-researchmetagenomicsvirulence-factorrecombinationpangenomicsrgiantimicrobial-resistancelateral-gene-transfer
      Python
      •
      MIT License
      •7•28•3•0•Updated Feb 19, 2026Feb 19, 2026

    • beiko-lab.github.io

      Public
      SCSS
      •
      MIT License
      •0•0•0•0•Updated Jan 2, 2026Jan 2, 2026

    • sarand

      Public
      To extract AMR genes and their neighborhood
      Python
      •
      GNU General Public License v3.0
      •5•3•1•0•Updated Jul 30, 2025Jul 30, 2025

    • amr_name_datasets

      Public
      Scripts and supplementary files for Beiko et al., "Inconsistent naming of carbapenemase1 and colistin-resistance genes"
      MIT License
      •0•0•0•0•Updated Dec 19, 2024Dec 19, 2024

    • evolCCM

      Public
      R package for CCM (Community Coevolution Model)
      R
      •
      GNU General Public License v3.0
      •1•0•1•1•Updated Oct 28, 2024Oct 28, 2024

    • ARETE-page

      Public
      Static website for ARETE project information
      HTML
      •
      Apache License 2.0
      •0•0•0•0•Updated Mar 5, 2024Mar 5, 2024

    • Indizio

      Public
      A visual analytics tool to investigate correlated data structures using heatmaps, networks, and network statistics.
      Python
      •
      MIT License
      •2•0•5•1•Updated Nov 9, 2023Nov 9, 2023

    • sarandV0

      Public
      Python
      •
      GNU General Public License v3.0
      •0•0•2•0•Updated Aug 31, 2023Aug 31, 2023

    • AMRtime

      Public
      Tool to predict the presence of antimicrobial resistance in clinical metagenomes
      Python
      •
      MIT License
      •2•7•2•0•Updated May 19, 2023May 19, 2023

    • CBW2021_Module2_16S_Analysis

      Public
      Shell
      •5•2•0•0•Updated Dec 5, 2022Dec 5, 2022

    • DNA_encoders

      Public
      Python
      •
      MIT License
      •0•1•0•0•Updated Oct 12, 2022Oct 12, 2022

    • efaecium-niche

      Public
      Code for reproducing e. faecium niche paper results.
      Jupyter Notebook
      •
      Apache License 2.0
      •0•1•0•0•Updated Mar 14, 2022Mar 14, 2022

    • Expositor

      Public
      Python
      •0•0•0•0•Updated Dec 10, 2021Dec 10, 2021

    • sarand_fullVersion

      Public
      To extract AMR genes and their neighborhood
      Python
      •
      GNU General Public License v3.0
      •0•3•2•0•Updated Dec 7, 2021Dec 7, 2021

    • RAD

      Public archive
      RAD reports from the Beiko lab students
      0•0•0•0•Updated Sep 29, 2020Sep 29, 2020

    • gene_neighborhoods_pipeline

      Public
      A software pipeline to simplify the analysis and visualization of gene neighborhoods.
      Python
      •1•0•0•0•Updated Sep 22, 2020Sep 22, 2020

    • QUOREM_geno-MIC

      Public
      QUOREM: Query, Unify, and Organize Research on the Ecology of Microorganisms
      HTML
      •4•1•1•0•Updated Jul 20, 2020Jul 20, 2020

    • training_resources

      Public
      Collation of useful training materials
      2•0•0•0•Updated Jun 12, 2020Jun 12, 2020

    • mockrobiota

      Public
      A public resource for microbiome bioinformatics benchmarking using artificially constructed (i.e., mock) communities.
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •34•0•0•0•Updated May 20, 2020May 20, 2020

    • 2020-BioinformaticsAlgorithms

      Public
      Tutorial assignments for CSCI4181/CSCI6802 (2020 edition)
      Jupyter Notebook
      •2•2•0•0•Updated Feb 2, 2020Feb 2, 2020

    • RADProc

      Public
      Roff
      •
      GNU General Public License v3.0
      •1•3•1•0•Updated Dec 6, 2019Dec 6, 2019

    • q2-extractor

      Public
      A small utility that maintains functions to pry data out of QIIME artifact and visualization files and transform as needed.
      Python
      •
      MIT License
      •0•1•0•0•Updated Nov 21, 2019Nov 21, 2019

    • mimb_16S

      Public
      Repository containing scripts and files for 16S gene community analysis chapter in Methods in Molecular Biology
      Shell
      •8•25•1•0•Updated May 22, 2019May 22, 2019

    • ananke

      Public
      Ananke: Clustering marker gene data by time-series patterns
      Python
      •
      MIT License
      •2•10•4•0•Updated Apr 9, 2019Apr 9, 2019

    • CSCI4180_6801_2019

      Public
      Scripts and data for 2019's CSCI4180 and CSCI6801 class.
      Shell
      •
      MIT License
      •1•0•0•0•Updated Mar 28, 2019Mar 28, 2019

    • ananke-docs

      Public
      Beautiful static documentation for your API
      JavaScript
      •
      Other
      •21k•0•0•0•Updated Feb 19, 2019Feb 19, 2019

    • PMERGE

      Public
      C++
      •
      GNU General Public License v3.0
      •0•0•1•0•Updated Oct 2, 2018Oct 2, 2018

    • MEGASAT

      Public
      High-throughput analysis of targeted microsatellite sequences.
      Perl
      •3•4•3•1•Updated Oct 1, 2018Oct 1, 2018

    • q2-ebd

      Public
      A QIIME2 wrapper for the ExpressBetaDiversity program: https://github.com/dparks1134/ExpressBetaDiversity
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •44•0•0•0•Updated Aug 20, 2018Aug 20, 2018

    • gengis

      Public
      GenGIS (pronounced 'Genghis' like Genghis Khan) is a bioinformatics application that allows users to combine digital map data with information about biological …
      C++
      •
      GNU General Public License v3.0
      •12•29•18•0•Updated Nov 9, 2017Nov 9, 2017