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 (3.24)
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, 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 single-cell workflows.
Author: Nick Borcherding [aut, cre], Qile Yang [aut], Ksenia Safina [aut], Justin Reimertz [ctb]
Maintainer: Nick Borcherding <ncborch at gmail.com>
citation("scRepertoire")):Nick Borcherding, Qile Yang, Ksenia Safina. scRepertoire: A toolkit for single-cell immune receptor profiling. doi:10.18129/B9.bioc.scRepertoire, R package version 2.9.1, https://bioconductor.org/packages/scRepertoire.
Generated from the package metadata; it may differ from the package's own citation.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
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 | |
| LICENSE | Text |
Details
| biocViews | Annotation, Classification, ImmunoOncology, Sequencing, SingleCell, Software |
| Version | 2.9.1 |
| In Bioconductor since | BioC 3.12 (R-4.0) (6 years) |
| License | MIT + file LICENSE |
| Depends | ggplot2, R (>= 4.0) |
| Imports | BiocParallel, dplyr, evmix, ggalluvial, ggdendro, ggraph, grDevices, igraph, immApex (>= 1.7.1), iNEXT, Matrix, quantreg, Rcpp, rjson, rlang, S4Vectors, SeuratObject, SingleCellExperiment, SummarizedExperiment, tidygraph, purrr, lifecycle, methods |
| System Requirements | |
| URL | https://www.borch.dev/uploads/scRepertoire/ |
| Bug Reports | https://github.com/BorchLab/scRepertoire/issues |
See More
| Suggests | BiocManager, BiocStyle, circlize, dowser, knitr, Peptides, rmarkdown, scales, scater, Seurat, spelling, testthat (>= 3.0.0) |
| Linking To | Rcpp |
| Enhances | |
| Depends On Me | |
| Imports Me | Ibex |
| Suggests Me | dandelionR, immApex, immGLIPH, immLynx |
| Links To Me | |
| Build Report | Build Report, r-universe |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | scRepertoire_2.9.1.tar.gz |
| Windows Binary (x86_64) | scRepertoire_2.9.1.zip |
| macOS Binary (big-sur-x86_64) | scRepertoire_2.9.1.tgz |
| macOS Binary (sonoma-arm64) | scRepertoire_2.9.1.tgz |
| 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 |