scRepertoire

This is the development version of scRepertoire; for the stable release version, see scRepertoire.

A toolkit for single-cell immune receptor profiling

Bioconductor version: Development (3.19)

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")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("scRepertoire")

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

Documentation


Reference Manual	PDF

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	Annotation, Classification, ImmunoOncology, Sequencing, SingleCell, Software
Version	1.99.1
In Bioconductor since	BioC 3.12 (R-4.0) (3.5 years)
License	MIT + file LICENSE
Depends	ggplot2, R (>= 4.0)
Imports	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
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
Links To Me
Build Report	Build Report

Package Archives

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

Source Package
Windows Binary
macOS Binary (x86_64)
macOS Binary (arm64)
Source Repository	git clone https://git.bioconductor.org/packages/scRepertoire
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/scRepertoire
Package Short Url	https://bioconductor.org/packages/scRepertoire/
Package Downloads Report	Download Stats