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    53 repositories

    • vdjdb-db

      Public
      🗂️ [vdjdb.cdr3.net is up and running] Git-based TCR database storage & management. Submissions welcome!
      bioinformaticsdatabaseimmunologyt-cellantigen
      Groovy
      •
      Other
      •27•132•80•0•Updated Nov 15, 2024Nov 15, 2024

    • mirpy

      Public
      Python library and snippets for AIRR-seq data analysis, based on our in-house scripts
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Nov 12, 2024Nov 12, 2024

    • tcren-ms

      Public
      📝 [Paper] TCRen: predicting TCR-peptide recognition based on residue-level pairwise statistical potential
      Parrot
      •
      Other
      •4•13•1•0•Updated Nov 4, 2024Nov 4, 2024

    • tcremp

      Public
      T-cell receptor sequence embedding via prototypes
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •1•0•0•0•Updated Oct 15, 2024Oct 15, 2024

    • antigenomics.github.io

      Public
      🌐 Immuno Sequencing Algorithms Group web page
      JavaScript
      •
      Creative Commons Attribution 4.0 International
      •0•0•0•0•Updated Jul 22, 2024Jul 22, 2024

    • vdjdb-web

      Public
      Interactive browser for the VDJdb database
      HTML
      •
      Apache License 2.0
      •1•14•9•3•Updated May 25, 2024May 25, 2024

    • tcr-covid-classifier

      Public
      TCR motifs associated with infectious conditions and HLAs
      Jupyter Notebook
      •0•0•0•0•Updated May 16, 2024May 16, 2024

    • vdjtrack

      Public
      📝 Detecting T-cell expansion and quantifying clone survival from deep profiling of immune repertoires
      TeX
      •
      Apache License 2.0
      •0•0•0•0•Updated Feb 29, 2024Feb 29, 2024

    • pyigmap-old

      Public archive
      A smart wrapper for V(D)J mapping software
      Python
      •
      GNU General Public License v3.0
      •0•1•0•0•Updated Jan 31, 2024Jan 31, 2024

    • vdjdb-structure

      Public
      🗂️ Template-based modelling of TCR:pMHC structures for VDJdb database
      HTML
      •
      Apache License 2.0
      •1•0•0•0•Updated Jul 14, 2023Jul 14, 2023

    • tcr-thymic-selection

      Public
      Network properties of public TCRs
      Jupyter Notebook
      •0•1•0•0•Updated Jul 1, 2023Jul 1, 2023

    • mir

      Public
      A tool to handle immunogenomics data: from V/J references to AIRR-seq and TCR:pMHC structures.
      Java
      •0•0•0•0•Updated Apr 11, 2023Apr 11, 2023

    • milib

      Public
      ⚙️ (internal) Milib library
      Java
      •
      Apache License 2.0
      •0•0•0•0•Updated Apr 9, 2023Apr 9, 2023

    • milib_unused

      Public archive
      MiLib: yet another Java library for Next Generation Sequencing (NGS) data processing
      Java
      •
      Apache License 2.0
      •2•0•0•0•Updated Apr 9, 2023Apr 9, 2023

    • arradb

      Public
      0•0•0•0•Updated Mar 25, 2023Mar 25, 2023

    • repseqio

      Public
      Utils for manipulations with RepSeq data. First step: utils to build V/D/J/C references.
      Java
      •
      Apache License 2.0
      •4•0•0•0•Updated Mar 7, 2023Mar 7, 2023

    • vdjdb-structure-tmp

      Public archive
      Visualization of known and modeled structures from VDJdb using contact maps
      Jupyter Notebook
      •
      Apache License 2.0
      •0•0•0•0•Updated Mar 1, 2023Mar 1, 2023

    • repertoire-embedding

      Public archive
      Analyzing network structure of the known TCR-cognate epitope map
      Jupyter Notebook
      •
      Apache License 2.0
      •0•0•0•0•Updated Feb 28, 2023Feb 28, 2023

    • hla-go-ms

      Public
      HLA ligandome and parent protein Gene Ontology associations
      0•0•1•0•Updated Mar 25, 2022Mar 25, 2022

    • vdjdb-motifs

      Public
      ⚙️ Motif inference for the VDJdb database
      R
      •0•5•0•0•Updated Mar 9, 2022Mar 9, 2022

    • bioinf-cov-classifier

      Public archive
      Classifying the status of COVID samples and SARS-CoV2-specific TCRs
      Jupyter Notebook
      •0•1•0•0•Updated Jun 1, 2021Jun 1, 2021

    • vdjsight

      Public
      [under development] Next-generation immunome browser
      TypeScript
      •0•3•0•14•Updated May 10, 2021May 10, 2021

    • tcr-survival-model

      Public
      T-cell sampling and survival model for HSCT and similar T-cell repertoire dynamics studies
      HTML
      •0•0•0•0•Updated Feb 10, 2021Feb 10, 2021

    • ilrfilter

      Public
      Immunoglobulin-like Read Filter
      Java
      •0•1•0•1•Updated Oct 13, 2020Oct 13, 2020

    • vdjdb-classifier-benchmark

      Public
      Jupyter Notebook
      •
      Apache License 2.0
      •0•5•0•0•Updated Oct 3, 2020Oct 3, 2020

    • covid19-tcr-analysis

      Public
      Identification and analysis of TCR motifs specific to SARS-CoV-2 epitopes
      HTML
      •1•2•0•0•Updated May 20, 2020May 20, 2020

    • tcr-annotation-methodology

      Public
      📝 [Paper/Tutorial] T-cell repertoire annotation and motif discovery
      TeX
      •
      Other
      •4•13•3•0•Updated May 1, 2020May 1, 2020

    • trab-pairing-study

      Public
      📝 [Paper] Studying pairing preferences between TCR alpha and beta chains
      0•2•0•0•Updated Dec 27, 2019Dec 27, 2019

    • vdjviz

      Public
      ⚙️ A lightweight immune repertoire browser
      bioinformaticsbrowserwebimmunologyrep-seq
      JavaScript
      •
      Other
      •10•27•12•0•Updated Dec 10, 2019Dec 10, 2019

    • ipred

      Public
      Antigen immunogenicity prediction
      Jupyter Notebook
      •1•5•0•0•Updated Nov 25, 2019Nov 25, 2019