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@csi-greifflab Greiff Lab – Computational Systems Immunology

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    20 repositories

    • Systematic-benchmarking-of-mass-spectrometry-based-antibody-sequencing-reveals-methodological-biases

      Public
      R
      •0•0•0•0•Updated Aug 7, 2025Aug 7, 2025

    • pepe-cli

      Public
      Tool to extract sequence representations from protein language models
      Python
      •
      MIT License
      •0•1•0•1•Updated Jul 21, 2025Jul 21, 2025

    • GAMA

      Public
      Python
      •
      Other
      •0•0•0•0•Updated Jul 14, 2025Jul 14, 2025

    • AbAgAL

      Public
      Jupyter Notebook
      •1•5•0•0•Updated Apr 18, 2025Apr 18, 2025

    • negative-class-optimization

      Public
      Jupyter Notebook
      •
      GNU Affero General Public License v3.0
      •0•2•0•1•Updated Mar 31, 2025Mar 31, 2025

    • T1D-TCR

      Public
      This repository contains the source code and associated resources developed for the research paper titled “Identification of a type 1 diabetes-associated T cell receptor repertoire signature from the human peripheral blood”. The code primarily focuses on analyzing TCR repertoire associated with Type 1 Diabetes.
      Python
      •
      GNU General Public License v3.0
      •1•1•0•0•Updated Mar 26, 2025Mar 26, 2025

    • developability_profiling

      Public
      Jupyter Notebook
      •6•23•3•0•Updated Jan 6, 2025Jan 6, 2025

    • global-epistasis

      Public
      Jupyter Notebook
      •2•0•0•0•Updated Dec 18, 2024Dec 18, 2024

    • airrtm

      Public
      Python
      •
      GNU General Public License v3.0
      •0•1•0•0•Updated Jul 17, 2024Jul 17, 2024

    • airrtm_data

      Public
      GNU General Public License v3.0
      •0•0•0•0•Updated Jul 16, 2024Jul 16, 2024

    • Absolut

      Public
      Unconstrained lattice antibody-antigen bindings generator
      Jupyter Notebook
      •21•110•7•0•Updated Jul 1, 2024Jul 1, 2024

    • Preexisting-immunity-influenza-mice

      Public
      Code, figures, and processed data for the manuscript
      0•0•0•0•Updated Feb 20, 2024Feb 20, 2024

    • manuscript_bulkseq-scseq-abseq_integration

      Public
      R
      •0•2•0•0•Updated Nov 2, 2023Nov 2, 2023

    • manuscript_short_motif_data_processing_supplementary

      Public
      Python
      •
      GNU Affero General Public License v3.0
      •0•0•0•0•Updated Oct 21, 2023Oct 21, 2023

    • manuscript_short_motif_experimental_computational_supplementary

      Public
      0•0•0•0•Updated Jun 12, 2023Jun 12, 2023

    • mwds_calculator

      Public
      Artificial Bee Colony - Estimation of Distribution Algorithm (ABC-EDA) is an algorithm to compute minimum weight dominating sets of undirected weighted networks. Adapted from Singh's and Shetgaonkar's publication, "Hybridization of Artificial Bee Colony Algorithm with Estimation of Distribution Algorithm for Minimum Weight Dominating Set Problem…
      Python
      •
      GNU Affero General Public License v3.0
      •1•3•0•0•Updated Feb 15, 2023Feb 15, 2023

    • desygnator

      Public
      desYgnator is a computational method for comparing AIRR-seq samples. deYgnator stands for DEtection of SYstematic differences in GeneratioN of Adaptive immune recepTOr Repertoires
      Jupyter Notebook
      •
      GNU Affero General Public License v3.0
      •0•0•0•0•Updated Sep 26, 2022Sep 26, 2022

    • manuscript_progress_challenges_on-demand_antibody

      Public
      Jupyter Notebook
      •1•5•0•0•Updated Aug 24, 2021Aug 24, 2021

    • manuscript_insilico_antibody_generation

      Public
      R
      •
      GNU Affero General Public License v3.0
      •7•23•2•0•Updated Jul 4, 2021Jul 4, 2021

    • HackathonCPH2021

      Public
      Repository for the Copenhagen Bioinformatics Hackathon 2021 Protein Edition. (VAE, CLustering)
      Python
      •1•0•0•0•Updated Apr 23, 2021Apr 23, 2021