Package: scRepertoire 2.9.0

Nick Borcherding

scRepertoire: A toolkit for single-cell immune receptor profiling

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, 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 single-cell workflows.

Authors:Nick Borcherding [aut, cre], Qile Yang [aut], Ksenia Safina [aut], Justin Reimertz [ctb]

# Install 'scRepertoire' in R:

install.packages('scRepertoire', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/borchlab/screpertoire/issues

Pkgdown/docs site:https://www.borch.dev

Uses libs:

c++– GNU Standard C++ Library v3

Datasets:

contig_list - A List of Eight Single-cell TCR Sequencing Runs.
scRep_example - A Seurat Object of 500 Single T cells,

On BioConductor:scRepertoire-2.9.0(bioc 3.24)scRepertoire-2.8.0(bioc 3.23)

software immunooncology singlecell classification annotation sequencing cpp

11.58 score 369 stars 1 packages 638 scripts 1.5k downloads 3 mentions 44 exports 112 dependencies

Last updated from:bebc413a50. Checks:4 WARNING, 10 OK. Indexed: yes.

Target	Result	Time
bioc-checks	WARNING	253
linux-devel-arm64	WARNING	699
linux-devel-x86_64	WARNING	748
source / vignettes	OK	556
linux-release-arm64	OK	670
linux-release-x86_64	OK	775
macos-release-arm64	OK	645
macos-release-x86_64	OK	1025
macos-oldrel-arm64	OK	537
macos-oldrel-x86_64	OK	1293
windows-devel	WARNING	822
windows-release	OK	735
windows-oldrel	OK	818
wasm-release	OK	193

Exports:addVariable alluvialClones annotateInvariant clonalAbundance clonalBias clonalBin clonalCluster clonalCompare clonalDiversity clonalHomeostasis clonalLength clonalNetwork clonalOccupy clonalOverlap clonalOverlay clonalProportion clonalQuant clonalRarefaction clonalScatter clonalSizeDistribution combineBCR combineExpression combineTCR createHTOContigList exportClones expression2List getCirclize getContigDoublets highlightClones loadContigs percentAA percentGenes percentGeneUsage percentKmer percentVJ positionalEntropy positionalProperty quietBCRgenes quietTCRgenes quietVDJgenes StartracDiversity subsetClones vizCirclize vizGenes

Dependencies:abind askpass base64enc BH Biobase BiocGenerics BiocParallel Biostrings cachem cli codetools cpp11 crayon curl DelayedArray digest dotCall64 dplyr evmix farver fastmap formatR futile.logger futile.options future future.apply generics GenomicRanges ggalluvial ggdendro ggforce ggplot2 ggraph ggrepel globals glue graphlayouts gridExtra gsl gtable httr igraph immApex immReferent iNEXT IRanges isoband jsonlite labeling lambda.r lattice lazyeval lifecycle listenv magrittr MASS Matrix MatrixGenerics MatrixModels matrixStats memoise mime openssl parallelly pillar pkgconfig plyr polyclip progressr purrr quantreg R6 RColorBrewer Rcpp RcppArmadillo RcppEigen reshape2 rjson rlang rvest S4Arrays S4Vectors S7 scales selectr Seqinfo SeuratObject SingleCellExperiment snow sp spam SparseArray SparseM stringi stringr SummarizedExperiment survival sys systemfonts tibble tidygraph tidyr tidyselect tweenr utf8 vctrs viridis viridisLite withr xml2 XVector yaml

Starting work with scRepertoire.

Nick Borcherding

Rendered fromvignette.Rmdusingknitr::rmarkdownon Jun 09 2026.

Last update: 2026-04-03
Started: 2020-01-18

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Adding Variables After combineTCR() or combineBCR()	addVariable
Alluvial Plotting for Single-Cell Object	alluvialClones
Annotate invariant T cells (MAIT or iNKT) in single-cell TCR data	annotateInvariant
Plot the Relative Abundance of Clones	clonalAbundance
Calculate Clonal Bias Towards a Cluster or Compartment	clonalBias
Bin Clones by Frequency or Proportion	clonalBin
Cluster clones by sequence similarity	clonalCluster
Compare Clonal Abundance Across Variables	clonalCompare
Calculate Clonal Diversity	clonalDiversity
Plot Clonal Homeostasis of the Repertoire	clonalHomeostasis
Plot the Distribution of Sequence Lengths	clonalLength
Visualize Clonal Network in Dimensional Reductions	clonalNetwork
Plot cloneSize by Variable in Single-Cell Objects	clonalOccupy
Examining the clonal overlap between groups or samples	clonalOverlap
Visualize Distribution of Clonal Frequency	clonalOverlay
Plot the Clonal Space Occupied by Specific Clones	clonalProportion
Plot Number or Proportions of Clones	clonalQuant
Calculate rarefaction based on the abundance of clones	clonalRarefaction
Scatter Plot Comparing Clones Across Two Samples	clonalScatter
Plot powerTCR Clustering Based on Clonal Size	clonalSizeDistribution
Combine B Cell Receptor Contig Data	combineBCR
Adding Clonal Information to Single-Cell Object	combineExpression
Combine T Cell Receptor Contig Data	combineTCR
A List of Eight Single-cell TCR Sequencing Runs.	contig_list
Deconvolute Contig Information from Multiplexed Experiments	createHTOContigList
Export Clonal Data in Various Formats	exportClones
Generate Data Frame to Plot Chord Diagram	getCirclize
Get Contig Doublets	getContigDoublets
Highlighting Specific Clones	highlightClones
Load Immune Receptor Sequencing Contigs	loadContigs
Plot Relative Amino Acid Composition by Position	percentAA
Summarizes and Visualizes Gene Usage	percentGenes percentGeneUsage percentVJ vizGenes
Analyze K-mer Motif Composition	percentKmer
Examining the Diversity of Amino Acids by Position	positionalEntropy
Plot Positional Physicochemical Property Analysis	positionalProperty
Remove TCR and BCR genes from variable gene results	quietBCRgenes quietBCRgenes.default quietBCRgenes.Seurat quietTCRgenes quietTCRgenes.default quietTCRgenes.Seurat quietVDJgenes
A Seurat Object of 500 Single T cells,	scRep_example
Calculate Startrac-based Diversity Indices	StartracDiversity
Subset The Product of combineTCR() or combineBCR()	subsetClones
Visualize Clonal Relationships as a Chord Diagram	vizCirclize