scRepertoire
This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see scRepertoire.
A toolkit for single-cell immune receptor profiling
Bioconductor version: 3.16
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("scRepertoire")):
Installation
To install this package, start R (version "4.2") 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 | ||
| NEWS | Text |
Details
| biocViews | Annotation, Classification, ImmunoOncology, Sequencing, SingleCell, Software |
| Version | 1.8.0 |
| In Bioconductor since | BioC 3.12 (R-4.0) (3.5 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 |
| System Requirements | |
| URL |
See More
| Suggests | knitr, rmarkdown, BiocStyle, circlize, scales, Seurat, scater |
| Linking To | |
| 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 | scRepertoire_1.8.0.tar.gz |
| Windows Binary | scRepertoire_1.8.0.zip |
| macOS Binary (x86_64) | scRepertoire_1.8.0.tgz |
| macOS Binary (arm64) | scRepertoire_1.8.0.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 3.16 | Source Archive |