What problem does it solve? Single-cell immune profiling generates complex VDJ contig data that is difficult to combine, quantify, and compare across samples. This Skill provides standardized R workflows for clonal expansion analysis, diversity metrics, VDJ gene usage, antigen prediction, and cross-tissue clonal sharing on FGCZ infrastructure. ## Core Features & Use Cases - Clonotype Assembly and Seurat Integration: Load CellRanger VDJ outputs (10x, AIRR, BD, MiXCR, TRUST4, WAT3R), combine contigs into clonotypes, and merge with Seurat transcriptomic objects. - Repertoire Analysis: Compute clonal expansion, diversity metrics (Shannon, Simpson, Chao1), Morisita-Horn overlap, VDJ gene usage, and STARTRAC migration indices. - Antigen Annotation: Annotate TCR sequences against VDJdb using Trex for epitope specificity prediction. - Use Case: Compare TCR repertoires between matched PBMC and skin samples to identify dual-expanded clones shared across tissues, then visualize them on UMAPs and alluvial diagrams. ## Quick Start Ask the agent to load the CellRanger VDJ filtered_contig_annotations.csv files for your samples, combine them into clonotypes with scRepertoire, and integrate the results into your Seurat object.
