An analysis aimed at providing a benchmark of the PIEMA tool for T cell receptor (TCR) structural similarity identification. This analysis also extends PIEMA through the implementation of multiple Logistic Regression classifiers incorporating sequence and structural features to make predictions on shared specificity between TCRs.

Clustering of immune receptor repertoires

A series of R scripts which can be used to 1) generate nonredundant benchmark datasets of paired-chain T cell receptor (TCR) binding data, and 2) visualize the various characteristics of this data.

Accompanying Repository to TCR-TRANSLATE paper.

Prediction of interferon-gamma inducing peptides using alignment-based and alignment-free methods

An improved method for predicting binders of HLA-DRB1-04:01

Simple Contrastive Embedding of the Primary sequence of T cell Receptors

Standardise TR/MH data

This Python script generates multi-epitope vaccine constructs by combining permutations of cytotoxic T lymphocyte (CTL), helper T lymphocyte (HTL), and B cell epitopes. It uses linkers and adjuvants to create unique constructs, which are saved in FASTA format for further analysis.

LZ76 Graphs and Applications in Immunology

Bayesian inference of Activation of TCR by Mutant Antigens

From raw dna to 3d representation of human antibodies

🐶 hlabud: HLA genotype analysis in R

Comparison of gene usage in immune repertoires under different biological conditions

🧬 Immunarch: an R Package for Fast and Painless Exploration of Single-cell and Bulk T-cell/Antibody Immune Repertoires

CDR3 clustering module providing a new method for fast and accurate clustering of large data sets of CDR3 amino acid sequences, and offering functionalities for downstream analysis of clustering results.

This GitHub repo supports a project, led by Delphine Galiana. It explores the innate immune response to viral infections, focusing on the role of plasmacytoid dendritic cells (pDCs) and the impact of alternative splicing in their antiviral response.

ESMDesign uses ESM-IF1 for the design of fragments within multichain proteins

Sequence-based prediction of peptide-TCR interactions using paired chain data