scRepertoire

This package is for version 3.21 of Bioconductor; for the stable, up-to-date release version, see scRepertoire.

A toolkit for single-cell immune receptor profiling

Bioconductor version: 3.21

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 "4.5") 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 2.4.0

In Bioconductor since BioC 3.12 (R-4.0) (5 years)

License MIT + file LICENSE

Depends ggplot2, R (>= 4.0)

Imports assertthat, cubature, dplyr, evmix, ggalluvial, ggdendro, ggraph, grDevices, igraph, iNEXT, plyr, quantreg, Rcpp, reshape2, rjson, rlang, S4Vectors, SeuratObject, SingleCellExperiment, stringr, stringdist, SummarizedExperiment, tidygraph, truncdist, VGAM, purrr, lifecycle, methods

System Requirements

URL https://www.borch.dev/uploads/scRepertoire/

Bug Reports https://github.com/BorchLab/scRepertoire/issues

Suggests BiocManager, BiocStyle, circlize, knitr, rmarkdown, scales, scater, Seurat, spelling, testthat (>= 3.0.0), vdiffr, withr

Linking To Rcpp

Enhances

Depends On Me

Imports Me

Suggests Me dandelionR, immApex

Links To Me

Build Report Build Report

Package Archives

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

Source Package scRepertoire_2.4.0.tar.gz

Windows Binary (x86_64) scRepertoire_2.4.0.zip

macOS Binary (x86_64) scRepertoire_2.4.0.tgz

macOS Binary (arm64) scRepertoire_2.4.0.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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