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    114 repositories

    • sofi_core_gitops

      Public
      GitOps configuration for the sofi_core Kubernetes cluster
      2•0•0•0•Updated Mar 13, 2025Mar 13, 2025

    • bio_api

      Public
      REST API for triggering bioinformatic calculations from SOFI
      Python
      •0•0•0•0•Updated Mar 13, 2025Mar 13, 2025

    • sofi_core

      Public
      Python
      •0•1•4•30•Updated Mar 13, 2025Mar 13, 2025

    • sofi-mr-server

      Public
      JavaScript
      •
      MIT License
      •1•0•0•5•Updated Mar 13, 2025Mar 13, 2025

    • bifrost_bridge

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

    • aedseo

      Public
      Automated and Early Detection of Seasonal Epidemic Onset
      R
      •
      Other
      •0•1•4•0•Updated Mar 12, 2025Mar 12, 2025

    • bifrost_chewbbaca

      Public
      Python
      •
      MIT License
      •1•1•0•0•Updated Mar 12, 2025Mar 12, 2025

    • bifrost_run_launcher

      Public
      Python
      •
      MIT License
      •0•0•0•0•Updated Mar 10, 2025Mar 10, 2025

    • GeneSNPdetector

      Public
      Python
      •0•0•0•0•Updated Mar 5, 2025Mar 5, 2025

    • diseasystore

      Public
      R package that provides a feature store tailored towards disease modelling
      R
      •
      GNU General Public License v3.0
      •2•4•6•1•Updated Mar 4, 2025Mar 4, 2025

    • AEF-DDF

      Public
      R
      •0•1•1•0•Updated Mar 4, 2025Mar 4, 2025

    • SCDB

      Public
      R package for maintaining data bases with slowly-changing-dimensions
      R
      •
      GNU General Public License v3.0
      •3•6•6•1•Updated Mar 4, 2025Mar 4, 2025

    • ssi_pingme

      Public
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Mar 4, 2025Mar 4, 2025

    • diseasy

      Public
      R
      •0•6•16•2•Updated Feb 28, 2025Feb 28, 2025

    • rmlst

      Public
      Python
      •0•0•0•0•Updated Feb 25, 2025Feb 25, 2025

    • ssi_analysis_utility

      Public
      Package for the species specific analysis WP6 MicrobeSeq
      Python
      •
      MIT License
      •0•1•0•0•Updated Feb 24, 2025Feb 24, 2025

    • bifrost_sp_cdiff

      Public
      Cdiff related analysis for the SOFI platform.
      typingbifrostsoficdiff
      Python
      •0•0•0•0•Updated Feb 24, 2025Feb 24, 2025

    • porA

      Public
      Scripts for porA amplicon analysis
      Python
      •0•0•0•0•Updated Feb 21, 2025Feb 21, 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 Feb 19, 2025Feb 19, 2025

    • bifrostlib

      Public
      Python API for bifrost
      Python
      •
      MIT License
      •1•0•3•0•Updated Feb 4, 2025Feb 4, 2025

    • bifrost_assemblatron

      Public
      Bifrost Component: Assemblatron - De-novo assembly of paired reads for QC and downstream Analysis purposes
      Python
      •
      MIT License
      •0•0•0•0•Updated Feb 3, 2025Feb 3, 2025

    • bifrost_amrfinderplus

      Public
      Python
      •
      MIT License
      •0•0•0•0•Updated Jan 23, 2025Jan 23, 2025

    • Staphylococcal_nasal_occupancy

      Public
      R scripts accompanying the manuscript "Staphylococcal occupancy within the human nasal microbiota" (Ingham et al.)
      0•0•0•0•Updated Jan 16, 2025Jan 16, 2025

    • calc-script-find_run_diff

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

    • 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_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•4•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