scRepertoire Documentation

scRepertoire is a toolkit designed to couple RNA quantification with immune cell receptor profiling (TCR/BCR) at the single-cell level.

It supports multiple single-cell clonal formats, including:

• 10x
• AIRR
• BD
• MiXCR
• TRUST4
• WAT3R

The framework is designed to interact with popular R-based single-cell data pipelines (such as Seurat) and provides extensions for deep learning-based analysis.

scRepertoire can be extended with deep-learning tools for immune receptor analysis:

• Trex: For deep-learning-based autoencoding of T cell receptors (TCR).
• Ibex: For B cell receptor (BCR) analysis.
• immApex: Used for building custom deep-learning models with immune receptors.

If you require the legacy version 1 of the toolkit, you can install it directly from GitHub using devtools.

devtools::install_github("BorchLab/scRepertoire@v1")

The standard workflow for using scRepertoire involves three main steps: combining contig data into clones, visualizing clonal frequency, and attaching that data to a single-cell object (like a Seurat object).

Note: This example assumes contig_list and scRep_example are already available in your environment.

library(scRepertoire)

# Load and combine contigs into clones
combined.TCR <- combineTCR(contig_list,
                           samples = c("P17B", "P17L", "P18B", "P18L",
                                       "P19B", "P19L", "P20B", "P20L"))

# Visualize clonal frequency
clonalQuant(combined.TCR, clone.call = "strict", chain = "both")

# Attach clonal data to a single-cell object
scRep_example <- combineExpression(combined.TCR, scRep_example)

The current stable version of scRepertoire is available through Bioconductor. Use BiocManager::install() to install it.

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("scRepertoire")

To install the development branch from GitHub, you must also install the required dependency immApex. Use remotes::install_github() to install both packages.

remotes::install_github(c("BorchLab/immApex", "BorchLab/scRepertoire@devel"))