Fig 1.
Schematic overview of the scRepertoire workflow and analyses.
Sequence alignments from standard pipelines or custom reconstruction methods are directly imported into scRepertoire, which performs filtering and pairing of B- or T-lymphocyte receptors. A variety of clonal analyses and visualizations are then available, with the resulting immune receptor data seamlessly attachable to single-cell RNA, protein, or chromatin assays processed via Seurat or SingleCellExperiment. scRepertoire also offers native compatibility with immApex, Trex, and Ibex, enabling deep-learning–based embeddings of scAIRR sequences for classifier development or multimodal data integration. The figure utilizes images from the NIAID BioArt (https://bioart.niaid.nih.gov/) repository under the CC-BY license.
Fig 2.
Single-cell analysis of lymphocytes in erythema migrans lesions and adjacent normal skin.
A. UMAP projection derived from single-cell RNA and TCR/BCR sequencing, revealing distinct lymphocyte subpopulations. B. UMAP overlay highlighting clonal expansion by relative frequency. Bar plots illustrate occupied clonal space, ranked by clone size and stratified by lymphocyte cell type. C. Alluvial plots showing TCR clones shared among erythema migrans lesions (SKL), adjacent normal skin (SKN), and blood (BL), featuring the top 20 clones per patient by repertoire proportion. D. Bootstrapped Shannon and inverse Simpson diversity values for each sequencing run with clonal rarefaction and extrapolation curves based on Shannon diversity indices. E. Proportion of amino acids and mean Atchley factor values across the heavy-chain CDR3 region for samples 192566 and 192567. F. Heatmap of TRAV gene usage alongside principal component analysis of sequencing runs. G. TRA chain clustering based on amino acid sequences using a normalized Levenshtein edit distance threshold (0.85), visualized on a UMAP and via a Fruchterman–Reingold layout in igraph. The dot size indicates the number of sequences or extent of clonal expansion.