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A toolkit for single-cell immune receptor profiling

Bioconductor version: Release (3.19)

scRepertoire is a toolkit for processing and analyzing single-cell T-cell receptor (TCR) and immunoglobulin (Ig). The scRepertoire framework supports use of 10x, AIRR, BD, MiXCR, Omniscope, TRUST4, and WAT3R single-cell formats. The functionality includes basic clonal analyses, repertoire summaries, distance-based clustering and interaction with the popular Seurat and SingleCellExperiment/Bioconductor R workflows.

Author: Nick Borcherding [aut, cre], Qile Yang [aut], Ksenia Safina [aut]

Maintainer: Nick Borcherding <ncborch at>

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


To install this package, start R (version "4.4") 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 2.0.0
In Bioconductor since BioC 3.12 (R-4.0) (3.5 years)
License MIT + file LICENSE
Depends ggplot2, R (>= 4.0)
Imports cubature, dplyr, evmix, ggalluvial, ggdendro, ggraph, grDevices, igraph, iNEXT, methods, plyr, quantreg, Rcpp, reshape2, rjson, rlang, S4Vectors, SeuratObject, SingleCellExperiment, stats, stringr, stringdist, SummarizedExperiment, tidygraph, truncdist, utils, VGAM, hash
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Suggests BiocManager, BiocStyle, circlize, knitr, rmarkdown, scales, scater, Seurat, spelling, testthat (>= 3.0.0), vdiffr
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Follow Installation instructions to use this package in your R session.

Source Package scRepertoire_2.0.0.tar.gz
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macOS Binary (x86_64) scRepertoire_2.0.0.tgz
macOS Binary (arm64) scRepertoire_2.0.0.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
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