scRepertoire

A toolkit for single-cell immune receptor profiling

Bioconductor version: Release (3.20)

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 gmail.com>

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

Installation

To install this package, start R (version "4.4") and enter:


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

BiocManager::install("scRepertoire")

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

Documentation

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

browseVignettes("scRepertoire")

Using scRepertoire	HTML	R Script
Reference Manual	PDF
NEWS	Text
LICENSE	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	Annotation, Classification, ImmunoOncology, Sequencing, SingleCell, Software
Version	2.2.1
In Bioconductor since	BioC 3.12 (R-4.0) (4 years)
License	MIT + file LICENSE
Depends	ggplot2, R (>= 4.0)
Imports	assertthat, 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, purrr, lifecycle
System Requirements
URL	https://www.borch.dev/uploads/scRepertoire/
Bug Reports	https://github.com/ncborcherding/scRepertoire/issues

Suggests	BiocManager, BiocStyle, circlize, knitr, rmarkdown, scales, scater, Seurat, spelling, testthat (>= 3.0.0), vdiffr
Linking To	Rcpp
Enhances
Depends On Me
Imports Me
Suggests Me	immApex
Links To Me
Build Report	Build Report

Package Archives

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

Source Package	scRepertoire_2.2.1.tar.gz
Windows Binary (x86_64)	scRepertoire_2.2.1.zip (64-bit only)
macOS Binary (x86_64)	scRepertoire_2.2.1.tgz
macOS Binary (arm64)	scRepertoire_2.2.1.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/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.20	Source Archive