Repositories list

• immuneML

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

  tcrbcrimmune-repertoire+ 5benchmarkingclassificationmachine-learning-analysisadaptive-immune-receptorsairr

  Python

  •

  GNU Affero General Public License v3.0

  •29•62•0•0•Updated Oct 25, 2024Oct 25, 2024

• 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•0•0•0•Updated Oct 22, 2024Oct 22, 2024

• 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•0•0•0•Updated Oct 17, 2024Oct 17, 2024

• immuneml_tools

  Public
  Galaxy tools using the immuneML conda package.

  Python

  •0•1•0•0•Updated Oct 13, 2024Oct 13, 2024

• stats_for_cs

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

  Jupyter Notebook

  •0•0•0•0•Updated Oct 11, 2024Oct 11, 2024

• crypt4gh

  Public
  Crypt4GH standard implementation

  bioinformaticsencryptioncrypt4gh

  Java

  •

  MIT License

  •6•2•2•11•Updated Oct 7, 2024Oct 7, 2024

• tsd-file-api-client

  Public
  TSD File API Client

  Java

  •

  MIT License

  •2•0•2•4•Updated Sep 19, 2024Sep 19, 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

• fdr_under_dependencies

  Public
  Jupyter Notebook

  •

  MIT License

  •0•3•0•0•Updated Sep 5, 2024Sep 5, 2024

• localega-tsd-proxy

  Public
  Java

  •

  MIT License

  •0•0•6•0•Updated Sep 4, 2024Sep 4, 2024

• dagsim

  Public
  A framework and specification language for simulating data based on graphical models

  simulationbayesian-networkcausal-models+ 2directed-acyclic-graphpython

  Python

  •

  GNU Affero General Public License v3.0

  •3•18•1•0•Updated Aug 28, 2024Aug 28, 2024

• StarSignDNA

  Public
  Python

  •

  MIT License

  •0•2•0•0•Updated Aug 26, 2024Aug 26, 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

  •8•19•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

• SimCal

  Public
  Simulation Calibration codebase for evaluating ML pipelines between real and learned worlds

  Python

  •

  Apache License 2.0

  •0•0•0•0•Updated Mar 22, 2024Mar 22, 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

• mq-interceptor

  Public
  RabbitMQ interceptor for LocalEGA

  Go

  •

  MIT License

  •0•0•5•0•Updated Nov 14, 2023Nov 14, 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 offline running and support for HPC cluster execution. It is made for Linux based systems and has been tested on SLURM cluster execution.

  masterthesis

  Python

  •

  GNU General Public License v3.0

  •1•0•0•0•Updated Oct 3, 2023Oct 3, 2023

• CausalAIRR

  Public
  Python

  •1•10•0•0•Updated Aug 22, 2023Aug 22, 2023

• compairr

  Public
  Comparison of Adaptive Immune Receptor Repertoires

  bioinformaticsimmunologyrep-seq+ 4immunoinformaticsimmune-repertoirerepertoire-analysisairr

  C++

  •

  GNU Affero General Public License v3.0

  •5•25•3•0•Updated Jun 16, 2023Jun 16, 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

• 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•1•0•0•Updated Oct 30, 2022Oct 30, 2022

• localega-proxy-webserver

  Public
  Java

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

• statistical_genomics_exercises

  Public
  HTML

  •1•1•0•0•Updated Oct 26, 2022Oct 26, 2022

• pharmacoepi_simulation_workshop

  Public
  The material for the simulation session at the (Epi)genetics in Pharmacoepidemiology workshop

  Jupyter Notebook

  •0•1•0•0•Updated Sep 26, 2022Sep 26, 2022

• lega-uploader

  Public
  LocalEGA Data Upload Tool

  Go

  •

  MIT License

  •0•0•0•3•Updated Sep 5, 2022Sep 5, 2022