screpcombiningexpression
Combine scTCR/BCR repertoire data with scRNA-seq expression data using `scRepertoire::combineExpression()`. This process integrates immune receptor information (CDR3 sequences, V(D)J genes, clonotypes) into a Seurat object's metadata, enabling clonotype-aware gene expression analysis.
npx skills add majiayu000/claude-skill-registry --skill screpcombiningexpression --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
# ScRepCombiningExpression Process Configuration ## Purpose Combine scTCR/BCR repertoire data with scRNA-seq expression data using `scRepertoire::combineExpression()`. This process integrates immune receptor information (CDR3 sequences, V(D)J genes, clonotypes) into a Seurat object's metadata, enabling clonotype-aware gene expression analysis. ## When to Use - When analyzing paired scTCR-seq + scRNA-seq data or paired scBCR-seq + scRNA-seq data - Required for all downstream TCR/BCR analyses (CDR3Clustering, TESSA, ClonalStats) - After ScRepLoading and SeuratClustering (or TOrBCellSelection) - When you need to visualize or analyze clonotype distribution across RNA clusters ## Configuration Structure ### Process Enablement ```toml [ScRepCombiningExpression] cache = true ``` ### Input Specification ```toml [ScRepCombiningExpression.in] # Required inputs screpfile = ["ScRepLoading"] # scRepertoire object from ScRepLoading srtobj = ["SeuratClustering"] # Seurat object with RNA data ``` **Note**: Barcodes in `srtobj` must match barcodes in `screpfile`. Ensure both datasets were generated from the same cell calling run. ### Environment Variables ```toml [ScRepCombiningExpression.envs] # C
- Purpose
- When to Use
- Configuration Structure
- Process Enablement
- Input Specification
- Environment Variables
- Configuration Examples
- Minimal Configuration
- Standard TCR Integration
- BCR Heavy+Light Chain Integration
- Clonotype by RNA Cluster
- Remove Non-Productive Cells
- Gene-Based Clonotype Definition
- Common Patterns
What does the screpcombiningexpression skill do?
Combine scTCR/BCR repertoire data with scRNA-seq expression data using `scRepertoire::combineExpression()`. This process integrates immune receptor information (CDR3 sequences, V(D)J genes, clonotypes) into a Seurat object's metadata, enabling clonotype-aware gene expression analysis.
How do I install it?
Run `npx skills add majiayu000/claude-skill-registry --skill screpcombiningexpression --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From majiayu000/claude-skill-registry, a repository with 534 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.