AntigenOmics

vdjdb-db

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

vdjviz

⚙️ A lightweight immune repertoire browser

vdjdb-web

Interactive browser for the VDJdb database

tcr-annotation-methodology

📝 [Paper/Tutorial] T-cell repertoire annotation and motif discovery

tcren-ms

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

vdjdb-classifier-benchmark

vdjdb-motifs

⚙️ Motif inference for the VDJdb database

ipred

Antigen immunogenicity prediction

segment-parser

A parser for immune receptor gene data, mainly IMGT references

vdjsight

[under development] Next-generation immunome browser

covid19-tcr-analysis

Identification and analysis of TCR motifs specific to SARS-CoV-2 epitopes

trab-pairing-study

📝 [Paper] Studying pairing preferences between TCR alpha and beta chains

antigenomics.github.io

🌐 Immuno Sequencing Algorithms Group web page

bioinf-cov-classifier

Classifying the status of COVID samples and SARS-CoV2-specific TCRs

ilrfilter

Immunoglobulin-like Read Filter

pyigmap

A smart wrapper for V(D)J mapping software

tcr-thymic-selection

Network properties of public TCRs

arradb

hla-go-ms

HLA ligandome and parent protein Gene Ontology associations

milib

⚙️ (internal) Milib library

milib_unused

MiLib: yet another Java library for Next Generation Sequencing (NGS) data processing

mir

A tool to handle immunogenomics data: from V/J references to AIRR-seq and TCR:pMHC structures.

mirpy

Python library and snippets for AIRR-seq data analysis, based on our in-house scripts

repertoire-embedding

Analyzing network structure of the known TCR-cognate epitope map

repseqio

Utils for manipulations with RepSeq data. First step: utils to build V/D/J/C references.

tcr-covid-classifier

TCR motifs associated with infectious conditions and HLAs

tcr-survival-model

T-cell sampling and survival model for HSCT and similar T-cell repertoire dynamics studies

vdjdb-structure

🗂️ Template-based modelling of TCR:pMHC structures for VDJdb database

vdjdb-structure-tmp

Visualization of known and modeled structures from VDJdb using contact maps

vdjtrack

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