Repositories list

• vdjdb-db

  Public
  🗂️ [vdjdb.cdr3.net is up and running] Git-based TCR database storage & management. Submissions welcome!

  bioinformaticsdatabaseimmunology+ 2t-cellantigen

  Python

  •

  Other

  •26•138•82•0•Updated Aug 6, 2025Aug 6, 2025

• tcremp

  Public
  T-cell receptor sequence embedding via prototypes

  Jupyter Notebook

  •

  GNU General Public License v3.0

  •1•5•2•0•Updated Aug 6, 2025Aug 6, 2025

• tcrenc

  Public
  TCR sequence (auto)encoders

  HTML

  •0•0•0•0•Updated Aug 5, 2025Aug 5, 2025

• vdjmatch2

  Public
  WIP, replaces vdjmatch

  C++

  •2•0•0•0•Updated Jul 30, 2025Jul 30, 2025

• 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

  •3•1•0•0•Updated Jul 29, 2025Jul 29, 2025

• vdjdb-db-validation

  Public
  📝 [Commentary] Infographics for VDJdb records validation

  HTML

  •0•0•0•0•Updated Jul 28, 2025Jul 28, 2025

• vdjdb-web

  Public
  Interactive browser for the VDJdb database

  HTML

  •

  Apache License 2.0

  •1•14•9•3•Updated May 29, 2025May 29, 2025

• tcren-ms

  Public
  📝 [Paper] TCRen: predicting TCR-peptide recognition based on residue-level pairwise statistical potential

  Parrot

  •

  Other

  •4•19•1•0•Updated Mar 28, 2025Mar 28, 2025

• tcr-covid-classifier

  Public
  TCR motifs associated with infectious conditions and HLAs

  Jupyter Notebook

  •0•0•0•0•Updated Mar 27, 2025Mar 27, 2025

• vdjbet

  Public
  ⚙️ VDJ biomarker enrichment test

  HTML

  •0•0•0•0•Updated Mar 17, 2025Mar 17, 2025

• 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

• vdjtrack

  Public
  📝 Detecting T-cell expansion and quantifying clone survival from deep profiling of immune repertoires

  TeX

  •

  Apache License 2.0

  •0•1•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•1•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