scRepertoire
A toolkit for single-cell immune receptor profiling
Bioconductor version: 3.24 · Package version: 2.9.1
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
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.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("scRepertoire")Details
| Maintainer | Nick Borcherding <ncborch@gmail.com> |
| Author | Nick Borcherding [aut, cre], Qile Yang [aut], Ksenia Safina [aut], Justin Reimertz [ctb] |
| License | MIT + file LICENSE |
| URL | https://www.borch.dev/uploads/scRepertoire/ |
| Bug Reports | https://github.com/BorchLab/scRepertoire/issues |
| Source branch | devel |
| Build report | Bioconductor build system, r-universe |
| biocViews | Annotation, Classification, ImmunoOncology, Sequencing, SingleCell, Software |
| Package Short Url | https://bioconductor.org/packages/scRepertoire/ |
Citation
From within R, enter 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.
Documentation
Download
Follow the 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 (arm64) | scRepertoire_2.9.1.tgz |
| macOS binary (x86_64) | scRepertoire_2.9.1.tgz |
Dependencies
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
LinkingTo: Rcpp
Suggests: BiocManager, BiocStyle, circlize, dowser, knitr, Peptides, rmarkdown, scales, scater, Seurat, spelling, testthat (>= 3.0.0)