CellaRepertorium

DOI: 10.18129/B9.bioc.CellaRepertorium    

Data structures, clustering and testing for single cell immune receptor repertoires (scRNAseq RepSeq/AIRR-seq)

Bioconductor version: Release (3.13)

Methods to cluster and analyze high-throughput single cell immune cell repertoires, especially from the 10X Genomics VDJ solution. Contains an R interface to CD-HIT (Li and Godzik 2006). Methods to visualize and analyze paired heavy-light chain data. Tests for specific expansion, as well as omnibus oligoclonality under hypergeometric models.

Author: Andrew McDavid [aut, cre], Yu Gu [aut], Erik VonKaenel [aut], Thomas Lin Pedersen [ctb]

Maintainer: Andrew McDavid <Andrew_McDavid at urmc.rochester.edu>

Installation

To install this package, start R (version "4.1") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("CellaRepertorium")

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("CellaRepertorium")

 

HTML	R Script	An Introduction to CellaRepertorium
HTML	R Script	Clustering and differential usage of repertoire CDR3 sequences
HTML	R Script	Combining Repertoire with Expression with SingleCellExperiment
HTML	R Script	Quality control and Exploration of UMI-based repertoire data
PDF		Reference Manual
Text		NEWS

Details

biocViews	Clustering, ImmunoOncology, RNASeq, SingleCell, Software, TargetedResequencing, Technology, Transcriptomics
Version	1.2.0
In Bioconductor since	BioC 3.12 (R-4.0) (1 year)
License	GPL-3
Depends	R (>= 4.0)
Imports	dplyr, tibble, stringr, Biostrings, Rcpp, reshape2, methods, rlang (>= 0.3), purrr, Matrix, S4Vectors, BiocGenerics, tidyr, forcats, progress, stats, utils
LinkingTo	Rcpp
Suggests	testthat, readr, knitr, rmarkdown, ggplot2, BiocStyle, ggdendro, broom, lme4, RColorBrewer, SingleCellExperiment, scater, broom.mixed, cowplot
SystemRequirements
Enhances
URL	https://github.com/amcdavid/CellaRepertorium
BugReports	https://github.com/amcdavid/CellaRepertorium/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	CellaRepertorium_1.2.0.tar.gz
Windows Binary	CellaRepertorium_1.2.0.zip (32- & 64-bit)
macOS 10.13 (High Sierra)	CellaRepertorium_1.2.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/CellaRepertorium
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/CellaRepertorium
Package Short Url	https://bioconductor.org/packages/CellaRepertorium/
Package Downloads Report	Download Stats