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    110 repositories

    • bifrost_bridge

      Public
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Jan 13, 2025Jan 13, 2025

    • SCDB

      Public
      R package for maintaining data bases with slowly-changing-dimensions
      R
      •
      GNU General Public License v3.0
      •2•6•3•3•Updated Jan 13, 2025Jan 13, 2025

    • calc-script-find_run_diff

      Public
      Jupyter Notebook
      •0•0•0•0•Updated Jan 13, 2025Jan 13, 2025

    • cdiff_fbi

      Public
      Typing of Clostridioides difficile isolates using NGS data (reads and contigs) based on tandem repeat loci (TR6, TR10), and toxin genes (cdtA, cdtB, tcdA, tcdB, tcdC).
      typingtandem-repeatsfbitoxinscdiff
      ASP.NET
      •
      MIT License
      •0•0•0•0•Updated Jan 13, 2025Jan 13, 2025

    • diseasy

      Public
      R
      •0•6•18•6•Updated Jan 13, 2025Jan 13, 2025

    • diseasystore

      Public
      R package that provides a feature store tailored towards disease modelling
      R
      •
      GNU General Public License v3.0
      •2•4•5•3•Updated Jan 13, 2025Jan 13, 2025

    • AEF-DDF

      Public
      R
      •0•1•0•2•Updated Jan 13, 2025Jan 13, 2025

    • bifrost_chewbbaca

      Public
      Python
      •
      MIT License
      •1•1•0•0•Updated Jan 13, 2025Jan 13, 2025

    • sofi_core

      Public
      Python
      •0•1•4•29•Updated Jan 10, 2025Jan 10, 2025

    • aedseo

      Public
      Automated and Early Detection of Seasonal Epidemic Onset
      R
      •
      Other
      •0•1•6•0•Updated Jan 10, 2025Jan 10, 2025

    • sofi_core_gitops

      Public
      GitOps configuration for the sofi_core Kubernetes cluster
      2•0•0•0•Updated Jan 9, 2025Jan 9, 2025

    • bifrost_sp_ecoli

      Public
      Ecoli related analysis for the SOFI platform.
      typingbifrostecolisofi
      Python
      •0•0•0•0•Updated Jan 9, 2025Jan 9, 2025

    • bifrost_salmonella_subspecies_dtartrate

      Public
      Python
      •
      MIT License
      •0•0•0•0•Updated Jan 9, 2025Jan 9, 2025

    • bio_api

      Public
      REST API for triggering bioinformatic calculations from SOFI
      Python
      •0•0•0•4•Updated Jan 8, 2025Jan 8, 2025

    • bifrost_amrfinderplus

      Public
      Python
      •
      MIT License
      •0•0•0•0•Updated Dec 20, 2024Dec 20, 2024

    • project-covid19_subgenomic

      Public
      Scripts for identification of SARS-CoV-2 subgenomic RNA reads from BAM alignment files and subsequent statistical analyses.
      R
      •0•0•0•0•Updated Dec 19, 2024Dec 19, 2024

    • bifrost_sp_cdiff

      Public
      Cdiff related analysis for the SOFI platform.
      typingbifrostsoficdiff
      Python
      •0•0•0•0•Updated Dec 18, 2024Dec 18, 2024

    • bifrost_enterobase

      Public
      Python
      •
      MIT License
      •0•0•0•0•Updated Dec 18, 2024Dec 18, 2024

    • CD-MRG-PlatePlanner

      Public
      Python package to create multi-well plate layouts for specimen sample data. Automatically distributes quality control samples according to scheme in config file.
      Python
      •
      MIT License
      •1•3•0•3•Updated Dec 17, 2024Dec 17, 2024

    • bifrost_cge_resfinder

      Public
      Bifrost Component: CGE Resfinder - Runs kma on resfinder DB using paired reads
      Python
      •
      MIT License
      •1•0•0•0•Updated Dec 13, 2024Dec 13, 2024

    • sofi-mr-server

      Public
      JavaScript
      •
      MIT License
      •1•0•0•5•Updated Dec 12, 2024Dec 12, 2024

    • microreact_integration

      Public
      Python code for integrating with Microreact
      Python
      •
      MIT License
      •0•3•0•1•Updated Nov 30, 2024Nov 30, 2024

    • irida-uploader

      Public
      Sequence file uploader for IRIDA
      Python
      •
      Apache License 2.0
      •13•0•0•1•Updated Nov 26, 2024Nov 26, 2024

    • S_epidermidis_rpoB_point_mutations

      Public
      Investigation of novel rpoB mutations associated with reduced sensitivity to rifampicin and vancomycin
      0•0•0•0•Updated Nov 25, 2024Nov 25, 2024

    • GeneSNPdetector

      Public
      Python
      •0•0•0•0•Updated Nov 21, 2024Nov 21, 2024

    • ecoli_fbi

      Public
      Determines the serotype and virulence in Escherichia coli isolates using NGS data (reads) through kmer alignment.
      genesecolivirulencefbiserotype
      Python
      •0•0•0•0•Updated Nov 20, 2024Nov 20, 2024

    • bifrost_seqsero

      Public
      Component for running seqsero in Bifrost
      Python
      •
      MIT License
      •0•0•0•0•Updated Nov 19, 2024Nov 19, 2024

    • bifrost_run_launcher

      Public
      Python
      •
      MIT License
      •0•0•0•0•Updated Nov 11, 2024Nov 11, 2024

    • microbeseq_nbdev_augment

      Public
      Files to assist in setup of nbdev
      templategetting-started
      Jupyter Notebook
      •
      MIT License
      •1•0•0•0•Updated Oct 25, 2024Oct 25, 2024

    • Staphylococcal_nasal_occupancy

      Public
      R scripts accompanying the manuscript "Staphylococcal occupancy within the human nasal microbiota" (Ingham et al.)
      0•0•0•0•Updated Oct 16, 2024Oct 16, 2024