ScRep Combining Expression

What it does

ScRep Combining Expression integrates immune-receptor (TCR/BCR) metadata — CDR3 sequences, V(D)J gene calls, clonotype counts and proportions — into a Seurat object's metadata using scRepertoire::combineExpression(). The result enables clonotype-aware downstream analyses such as clonotype distribution across RNA clusters, clonal expansion summaries, and inputs for tools like CDR3Clustering and ClonalStats.

When to use it

Use this process when you have paired single-cell receptor sequencing (scTCR-seq or scBCR-seq) and scRNA-seq data from the same cells and need to: integrate receptor calls into Seurat metadata, calculate clonotype frequencies by sample or cluster, filter non-productive cells, or prepare inputs for clonotype-centric analyses and visualizations. Typical placement is after ScRepLoading and SeuratClustering (or TOrBCellSelection).

What's included

• Scripts: none bundled (process is configuration-driven)
• References: inline documentation and scRepertoire combineExpression links
• Instructions: TOML config examples for minimal, TCR-standard, BCR-heavy+light, cluster-based frequency, and filtering non-productive cells. Explains environment variables (cloneCall, chain, group_by, proportion, filterNA, cloneSize) and validation rules such as barcode matching.

Compatible agents

Compatible with analytic and pipeline orchestration agents that can run R-based single-cell workflows or compose pipeline steps (CI/pipeline agents, workflow runners). The core operations assume availability of R and scRepertoire within the analysis environment.