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A toolkit for single-cell immune receptor profiling

Bioconductor version: Release (3.18)

scRepertoire was built to process data derived from the 10x Genomics Chromium Immune Profiling for both T-cell receptor (TCR) and immunoglobulin (Ig) enrichment workflows and subsequently interacts with the popular Seurat and SingleCellExperiment R packages. It also allows for general analysis of single-cell clonotype information without the use of expression information. The package functions as a wrapper for Startrac and powerTCR R packages.

Author: Nick Borcherding [aut, cre]

Maintainer: Nick Borcherding <ncborch at gmail.com>

Citation (from within R, enter citation("scRepertoire")):


To install this package, start R (version "4.3") and enter:

if (!require("BiocManager", quietly = TRUE))


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

Using scRepertoire HTML R Script
Reference Manual PDF


biocViews Annotation, Classification, ImmunoOncology, Sequencing, SingleCell, Software
Version 1.12.0
In Bioconductor since BioC 3.12 (R-4.0) (3.5 years)
License GPL-2
Depends ggplot2, R (>= 4.0)
Imports stringdist, dplyr, reshape2, ggalluvial, stringr, vegan, powerTCR, SingleCellExperiment, SummarizedExperiment, plyr, parallel, doParallel, methods, utils, rlang, igraph, ggraph, tidygraph, SeuratObject
System Requirements
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Suggests knitr, rmarkdown, BiocStyle, circlize, scales, Seurat, scater
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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package scRepertoire_1.12.0.tar.gz
Windows Binary scRepertoire_1.12.0.zip
macOS Binary (x86_64) scRepertoire_1.12.0.tgz
macOS Binary (arm64) scRepertoire_1.12.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/scRepertoire
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/scRepertoire
Bioc Package Browser https://code.bioconductor.org/browse/scRepertoire/
Package Short Url https://bioconductor.org/packages/scRepertoire/
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