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CellaRepertorium

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

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


Bioconductor version: Development (3.19)

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], Aaron Wagner [aut], Thomas Lin Pedersen [ctb]

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

Citation (from within R, enter citation("CellaRepertorium")):

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("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")
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 HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews Clustering, ImmunoOncology, RNASeq, SingleCell, Software, TargetedResequencing, Technology, Transcriptomics
Version 1.13.0
In Bioconductor since BioC 3.12 (R-4.0) (3.5 years)
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, generics, glue
System Requirements
URL https://github.com/amcdavid/CellaRepertorium
Bug Reports https://github.com/amcdavid/CellaRepertorium/issues
See More
Suggests testthat, readr, knitr, rmarkdown, ggplot2, BiocStyle, ggdendro, broom, lme4, RColorBrewer, SingleCellExperiment, scater, broom.mixed, cowplot, igraph, ggraph
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 CellaRepertorium_1.13.0.tar.gz
Windows Binary CellaRepertorium_1.13.0.zip
macOS Binary (x86_64) CellaRepertorium_1.13.0.tgz
macOS Binary (arm64) CellaRepertorium_1.13.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/CellaRepertorium
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/CellaRepertorium
Bioc Package Browser https://code.bioconductor.org/browse/CellaRepertorium/
Package Short Url https://bioconductor.org/packages/CellaRepertorium/
Package Downloads Report Download Stats