Skip to content

@uio-bmi Centre for Bioinformatics, University of Oslo

All

    Repositories list

    86 repositories

    • immuneML

      Public
      immuneML is a platform for machine learning analysis of adaptive immune receptor repertoire data.
      benchmarkingclassificationtcr
      benchmarkingclassificationtcrmachine-learning-analysisbcrimmune-repertoireadaptive-immune-receptorsairr
      Python
      •
      GNU Affero General Public License v3.0
      •31•76•0•1•Updated Oct 2, 2026Oct 2, 2026

    • immuneml_tools

      Public
      Galaxy tools using the immuneML conda package.
      Python
      •0•1•0•1•Updated Sep 30, 2026Sep 30, 2026

    • StarSignDNA

      Public
      Python
      •
      MIT License
      •1•4•0•0•Updated Sep 29, 2026Sep 29, 2026

    • AIRR-ML-BM-2025

      Public
      Python
      •0•0•0•0•Updated Aug 31, 2026Aug 31, 2026

    • stats_for_cs

      Public
      Accompanying notebooks for the new stats course for computer scientists with simulations
      Jupyter Notebook
      •0•1•0•0•Updated Jul 12, 2026Jul 12, 2026

    • adaptive_immune_profiling_challenge_2025

      Public
      Website for AIRR-ML-25: Adaptive Immune Profiling Challenge. Participants will predict immune repertoire labels (e.g. disease, healthy) and identify label-assoc…
      0•3•0•0•Updated Nov 25, 2025Nov 25, 2025

    • predict-airr

      Public
      Starter code template recommendation for the participants for structuring their implementations
      Python
      •12•7•0•0•Updated Nov 4, 2025Nov 4, 2025

    • SimCal

      Public
      Meta-simulation framework for evaluating ML method selection
      benchmarkingmachine-learningsimulation-framework
      benchmarkingmachine-learningsimulation-frameworksimulation-modeling
      Python
      •
      Apache License 2.0
      •0•0•0•0•Updated Sep 23, 2025Sep 23, 2025

    • fdr_under_dependencies

      Public
      Jupyter Notebook
      •
      MIT License
      •0•3•0•0•Updated Aug 5, 2025Aug 5, 2025

    • ligo

      Public
      LIgO is a tool for simulation of adaptive immune receptors and repertoires.
      simulationantibodytcr
      simulationantibodytcrbcrairr
      Python
      •
      GNU Affero General Public License v3.0
      •2•1•1•0•Updated May 27, 2025May 27, 2025

    • dagsim

      Public
      A framework and specification language for simulating data based on graphical models
      pythonsimulationbayesian-network
      pythonsimulationbayesian-networkcausal-modelsdirected-acyclic-graph
      Python
      •
      GNU Affero General Public License v3.0
      •3•19•1•0•Updated May 2, 2025May 2, 2025

    • compairr

      Public
      Comparison of Adaptive Immune Receptor Repertoires
      bioinformaticsimmunologyrep-seq
      bioinformaticsimmunologyrep-seqimmunoinformaticsimmune-repertoirerepertoire-analysisairr
      C++
      •
      GNU Affero General Public License v3.0
      •7•30•11•0•Updated Jan 29, 2025Jan 29, 2025

    • localega-tsd-proxy

      Public archive
      Java
      •
      MIT License
      •0•0•6•1•Updated Jan 22, 2025Jan 22, 2025

    • mq-interceptor

      Public archive
      RabbitMQ interceptor for LocalEGA
      Go
      •
      MIT License
      •0•0•0•0•Updated Jan 22, 2025Jan 22, 2025

    • crypt4gh

      Public archive
      Crypt4GH standard implementation
      bioinformaticsencryptioncrypt4gh
      bioinformaticsencryptioncrypt4gh
      Java
      •
      MIT License
      •6•2•1•6•Updated Jan 22, 2025Jan 22, 2025

    • pilot_data_analysis_AIRR_ML_BM_2025

      Public
      Scripts enabling the reproducibility of pilot data analysis carried out for AIRR-ML-BM-2025
      Python
      •0•0•0•0•Updated Jan 14, 2025Jan 14, 2025

    • IN-BIOSx000

      Public
      Course material for the IN-BIOSx000 course "Sequencing technologies, data analysis, and applications" at the University of Oslo
      Python
      •
      Creative Commons Zero v1.0 Universal
      •10•1•0•0•Updated Nov 12, 2024Nov 12, 2024

    • machine_learning_in_comp_bio_exercises

      Public
      These exercises are a part of the IN-BIOS5000 course at UiO, for the intro lectures on machine learning in computational biology.
      Jupyter Notebook
      •0•2•0•0•Updated Nov 8, 2024Nov 8, 2024

    • tsd-file-api-client

      Public archive
      TSD File API Client
      Java
      •
      MIT License
      •2•0•2•4•Updated Oct 30, 2024Oct 30, 2024

    • cookiecutter-python-research-project

      Public
      A cookiecutter for easier continous integration in a research project based on Python code
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•1•0•0•Updated Sep 18, 2024Sep 18, 2024

    • graph_peak_caller

      Public
      ChIP-seq peak caller for reads mapped to a graph-based reference genome
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •9•26•7•1•Updated Aug 17, 2024Aug 17, 2024

    • starsigndna-doc

      Public
      Python
      •0•0•0•0•Updated Aug 5, 2024Aug 5, 2024

    • kmercount

      Public
      Simple kmer counter using Bloom filter and efficient hash function
      C++
      •
      GNU Affero General Public License v3.0
      •1•2•3•0•Updated May 2, 2024May 2, 2024

    • LocalEGA-deploy-swarm-fork

      Public
      Docker Swarm deployment of LocalEGA
      Java
      •
      MIT License
      •2•0•0•0•Updated Jan 19, 2024Jan 19, 2024

    • SynthPwr

      Public
      Synthetic framework for stress testing the parameters and statistical power of epigenetic power calculators
      Python
      •
      MIT License
      •0•1•0•0•Updated Dec 7, 2023Dec 7, 2023

    • VirMake

      Public
      VirMake is a Snakemake based pipeline that offers viral metagenic data analysis on paired-end data. It offers taxonomic and functional annotation, supports offl…
      masterthesis
      masterthesis
      Python
      •
      GNU General Public License v3.0
      •1•0•0•0•Updated Oct 3, 2023Oct 3, 2023

    • CausalAIRR

      Public
      Python
      •1•9•0•0•Updated Aug 22, 2023Aug 22, 2023

    • numpy_alignments

      Public
      Simple Python module for efficient storing and comparison of mapped reads using numpy
      Python
      •0•2•0•0•Updated Mar 13, 2023Mar 13, 2023

    • python-types-examples

      Public
      Python
      •
      MIT License
      •0•0•0•0•Updated Feb 14, 2023Feb 14, 2023

    • localega-broker

      Public
      Shell
      •
      MIT License
      •0•1•2•0•Updated Feb 8, 2023Feb 8, 2023
    ProTip! When viewing an organization's repositories, you can use the props. filter to filter by custom property.