screpcombiningexpression

You can integrate TCR or BCR repertoire data with scRNA-seq by enriching the Seurat object's metadata with clonotype information like CTgene, CTnt, and CTaa. This process enables clonotype-aware gene expression analysis after initial Seurat clustering.

Combining scRNA-seq and VDJ data adds clonotype metadata such as CTgene, CTnt, CTaa, CTcount, CTfrequency, CTproportion, and VDJ_Presence to the Seurat object. These fields allow diverse downstream analyses like CDR3 clustering and clonal statistics.

Yes, you can customize clonotype definitions when merging scTCR-seq and scRNA-seq data by configuring parameters like cloneCall, chain, and group_by. This flexible configuration supports diverse study designs based on amino acid, nucleotide, or gene-level definitions.

Yes, you need to run ScRepLoading and SeuratClustering on your paired scTCR/BCR and scRNA-seq data before combining expression data. This prerequisite ensures the Seurat object is properly prepared to receive clonotype metadata enrichment.

After enriching Seurat metadata with clonotype information, downstream analyses such as CDR3 clustering, TESSA, and ClonalStats are supported. The enriched metadata enables direct correlation between immune receptor sequences and single-cell gene expression profiles.