scRepertoire

This package is for version 3.13 of Bioconductor; for the stable, up-to-date release version, see scRepertoire.

A toolkit for single-cell immune receptor profiling


Bioconductor version: 3.13

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 "4.1") 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 1.2.0
In Bioconductor since BioC 3.12 (R-4.0) (3.5 years)
License Apache License 2.0
Depends ggplot2, R (>= 4.0)
Imports Biostrings, dplyr, reshape2, ggalluvial, stringr, vegan, powerTCR, SummarizedExperiment, plyr, parallel, doParallel, methods, utils, rlang
System Requirements
URL
See More
Suggests knitr, rmarkdown, BiocStyle, scater, circlize, scales, Seurat
Linking To
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Depends On Me
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Build Report Build Report

Package Archives

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

Source Package scRepertoire_1.2.0.tar.gz
Windows Binary scRepertoire_1.2.0.zip
macOS 10.13 (High Sierra) scRepertoire_1.2.0.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/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.13 Source Archive