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

Need some help? Ask on the Bioconductor Support site!

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

Suggests knitr, rmarkdown, BiocStyle, scater, circlize, scales, Seurat

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Depends On Me

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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