scRepertoire

A toolkit for single-cell immune receptor profiling

Bioconductor version: Release (3.17)

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")):

Installation

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

Details

biocViews	Annotation, Classification, ImmunoOncology, Sequencing, SingleCell, Software
Version	1.10.1
In Bioconductor since	BioC 3.12 (R-4.0) (3 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, stats
Linking To
Suggests	knitr, rmarkdown, BiocStyle, circlize, scales, Seurat, scater
System Requirements
Enhances
URL

Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	scRepertoire_1.10.1.tar.gz
Windows Binary	scRepertoire_1.10.1.zip
macOS Binary (x86_64)	scRepertoire_1.10.1.tgz
macOS Binary (arm64)	scRepertoire_1.10.1.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 3.17	Source Archive