Repositories list

• stats_for_cs

  Public
  Accompanying notebooks for the new stats course for computer scientists with simulations

  Jupyter Notebook

  •0•0•0•0•Updated Feb 6, 2026Feb 6, 2026

• immuneML

  Public
  immuneML is a platform for machine learning analysis of adaptive immune receptor repertoire data.

  benchmarkingclassificationtcr+ 5machine-learning-analysisbcrimmune-repertoireadaptive-immune-receptorsairr

  Python

  •

  GNU Affero General Public License v3.0

  •30•74•0•0•Updated Feb 1, 2026Feb 1, 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

• StarSignDNA

  Public
  Python

  •

  MIT License

  •1•4•0•0•Updated Nov 25, 2025Nov 25, 2025

• predict-airr

  Public
  Starter code template recommendation for the participants for structuring their implementations

  Python

  •13•7•0•0•Updated Nov 4, 2025Nov 4, 2025

• SimCal

  Public
  Meta-simulation framework for evaluating ML method selection

  benchmarkingmachine-learningsimulation-framework+ 1simulation-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+ 2bcrairr

  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+ 2causal-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+ 4immunoinformaticsimmune-repertoirerepertoire-analysisairr

  C++

  •

  GNU Affero General Public License v3.0

  •7•28•10•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

  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

• immuneml_tools

  Public
  Galaxy tools using the immuneML conda package.

  Python

  •0•1•0•0•Updated Jan 9, 2025Jan 9, 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•25•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

  •3•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

  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

• localega-proxy-webserver

  Public
  Java

  •0•0•0•0•Updated Oct 27, 2022Oct 27, 2022