airr-seq

Generation probability, diversity, and simulation for AIRR-seq TCR/BCR repertoires, from graph models of decomposed receptor sequences. Python, C-accelerated.

[UNDER DEVELOPMENT] Pipeline for mapping and annotating T- and B-cell receptor gene rearrangement sequences

TCRscape - a tool for simultaneous multimodal gene expression and clonotype analysis of single T-cells profiled via the BD Rhapsody system.

Quality control scripts for AIRR-seq data

Barbera van Schaik, Antoine van Kampen: ENCORE project for analysis for T-cell and B-cell repertoires

Barbera van Schaik, Antoine van Kampen: REpertoire SEquence Data Analysis

Immunogenomics benchmark + skillset for AI agents

Rodrigo Garcia Valiente: Visual artsy representation of B-cell clonal repertoires using R

This repository contains bioinformatics workflows and Jupyter notebooks developed by the Molecular Virology and Vaccines Team (MVVT) for adaptive immune receptor repertoire sequencing (AIRR-seq) data. The workflows support B-cell receptor (BCR) repertoire analysis from bulk and single-cell sequencing data.

Data source tool for connecting a Galaxy instance to the immunological data bank iReceptor Plus Gateway.

Dasha Balashova, Antoine van Kampen, Barbera van Schaik: BCRCF