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    109 repositories

    • bio_api

      Public
      REST API for triggering bioinformatic calculations from SOFI
      Python
      •0•0•0•4•Updated Nov 8, 2024Nov 8, 2024

    • diseasystore

      Public
      R package that provides a feature store tailored towards disease modelling
      R
      •
      GNU General Public License v3.0
      •2•4•6•4•Updated Nov 8, 2024Nov 8, 2024

    • diseasy

      Public
      R
      •0•3•12•10•Updated Nov 8, 2024Nov 8, 2024

    • sofi_core

      Public
      Python
      •0•1•4•28•Updated Nov 7, 2024Nov 7, 2024

    • bifrost_amrfinderplus

      Public
      Python
      •
      MIT License
      •0•0•0•0•Updated Nov 7, 2024Nov 7, 2024

    • bifrost_sp_ecoli

      Public
      Ecoli related analysis for the SOFI platform.
      typingbifrostecolisofi
      Python
      •0•0•0•0•Updated Nov 7, 2024Nov 7, 2024

    • bifrost_run_launcher

      Public
      Python
      •
      MIT License
      •0•0•0•0•Updated Nov 7, 2024Nov 7, 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 6, 2024Nov 6, 2024

    • SCDB

      Public
      R package for maintaining data bases with slowly-changing-dimensions
      R
      •
      GNU General Public License v3.0
      •2•6•1•1•Updated Nov 6, 2024Nov 6, 2024

    • AEF-DDF

      Public
      R
      •0•1•0•1•Updated Nov 6, 2024Nov 6, 2024

    • aedseo

      Public
      Automated and Early Detection of Seasonal Epidemic Onset
      R
      •
      Other
      •0•1•6•0•Updated Nov 5, 2024Nov 5, 2024

    • bifrost_sp_cdiff

      Public
      Cdiff related analysis for the SOFI platform.
      typingbifrostsoficdiff
      Python
      •0•0•0•0•Updated Nov 4, 2024Nov 4, 2024

    • 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 Nov 1, 2024Nov 1, 2024

    • sofi_core_gitops

      Public
      GitOps configuration for the sofi_core Kubernetes cluster
      2•0•0•0•Updated Nov 1, 2024Nov 1, 2024

    • bifrost_chewbbaca

      Public
      Python
      •
      MIT License
      •1•1•0•0•Updated Oct 30, 2024Oct 30, 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

    • sofi-mr-server

      Public
      JavaScript
      •
      MIT License
      •1•0•0•4•Updated Oct 21, 2024Oct 21, 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

    • microreact_integration

      Public
      Python code for integrating with Microreact
      Python
      •
      MIT License
      •0•3•0•1•Updated Oct 7, 2024Oct 7, 2024

    • bifrostlib

      Public
      Python API for bifrost
      Python
      •
      MIT License
      •1•0•3•0•Updated Sep 23, 2024Sep 23, 2024

    • bifrost_whats_my_species

      Public
      Bifrost Component: Whats My Species - Checks species of sample and whether it's correct or not against a kraken DB
      Python
      •
      MIT License
      •0•0•0•0•Updated Sep 23, 2024Sep 23, 2024

    • bifrost_bridge

      Public
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Sep 17, 2024Sep 17, 2024

    • aeddo

      Public
      Automated and Early Detection of Disease Outbreaks
      R
      •
      Other
      •0•1•2•2•Updated Sep 3, 2024Sep 3, 2024

    • MicrobeSeq-Denmark

      Public
      Location for SSI's microbial surveillance pipelines
      SCSS
      •0•0•1•0•Updated Aug 9, 2024Aug 9, 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 Jul 30, 2024Jul 30, 2024

    • bps_fbi_sp_ecoli

      Public
      Ecoli species specific scripts in nbdev2 format.
      ecolifbibpsnbdev
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Jul 25, 2024Jul 25, 2024

    • refseq_fastq_downloader

      Public
      Python
      •
      Apache License 2.0
      •0•0•0•0•Updated Jul 2, 2024Jul 2, 2024

    • BPS_FBI_FSC_VirulenceFinder

      Public
      Bash scripts to run virulencefinder and serotypefinder in local settings on ecoli fasta and fastq.gz files.
      bashecoliassembliesrawreadsvirulencefinderserotypefinder
      Shell
      •0•0•0•0•Updated Jun 20, 2024Jun 20, 2024

    • microbeseq_nbdev_example

      Public
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Apr 19, 2024Apr 19, 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 Apr 10, 2024Apr 10, 2024