immuneML is a platform for machine learning analysis of adaptive immune receptor repertoire data.
Stitchr - a Python script to stitch together coding TCR nucleotide sequences from V, J, and CDR3 info
Highly informative TCR representation model
Standardise TR/MH/IG data
A database of T-cell receptor sequences
BASIC: BCR and TCR assembly from single cell RNA-seq
This is backend for CYRentBot
Alignment-free graph models of TCR and BCR repertoires built from Lempel-Ziv and FlashBack string decompositions. Compute sequence generation probability (Pgen) and repertoire diversity, and generate new sequences. Python with a C core.
Machine learning for Immune Repertoires
ESMDesign uses ESM-IF1 for the design of fragments within multichain proteins
Python SDK for Immune Epitope Database (IEDB) Analysis Tools API
Mining TCR:pMHC structural data
PepBridge for peptide-bridged, unified and structure-aware modeling of pMHC-TCR recognition
A machine learning method to predict TCR-peptide binding
Deep-learning V(D)J aligner for BCR and TCR sequences. A single model predicts V/D/J allele calls, segment boundaries and the junction, with AIRR-format output. Published in Nucleic Acids Research (2025).
LIgO is a tool for simulation of adaptive immune receptors and repertoires.
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