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screpcombiningexpression

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Integrate TCR/BCR data with RNA for clonotypes.

Data & Analytics#seurat#scrna-seq#tcr-bcr#clonotypes#screpertoire#vdj
Authorpwwang
Version1.0.0
Installs0

System Documentation

What problem does it solve?

This process enables the integration of immune receptor information (CDR3 sequences, V(D)J genes, clonotypes) with scRNA-seq expression data by enriching a Seurat object's metadata, allowing clonotype-aware gene expression analysis.

Core Features & Use Cases

  • Integrates TCR/BCR repertoires with scRNA-seq data to attach clonotype information to Seurat metadata.
  • Supports combining paired scTCR/BCR data with scRNA-seq data after ScRepLoading and SeuratClustering to enable downstream clonotype-based analyses.
  • Offers flexible configuration for clonotype definitions (aa, nt, gene, strict), chain selection, grouping, and filtering, enabling diverse study designs and downstream analyses such as CDR3 clustering, TESSA, and ClonalStats.

Quick Start

Configure ScRepCombiningExpression with ScRepLoading and SeuratClustering results to attach clonotype metadata to the Seurat object.

Dependency Matrix

Required Modules

None required

Components

Standard package

💻 Claude Code Installation

Recommended: Let Claude install automatically. Simply copy and paste the text below to Claude Code.

Please help me install this Skill:
Name: screpcombiningexpression
Download link: https://github.com/pwwang/immunopipe/archive/main.zip#screpcombiningexpression

Please download this .zip file, extract it, and install it in the .claude/skills/ directory.
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