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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 (3.18)

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 "4.3") 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 1.11.0
In Bioconductor since BioC 3.12 (R-4.0) (3 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
Linking To Rcpp
Suggests testthat, readr, knitr, rmarkdown, ggplot2, BiocStyle, ggdendro, broom, lme4, RColorBrewer, SingleCellExperiment, scater, broom.mixed, cowplot, igraph, ggraph
System Requirements
Enhances
URL https://github.com/amcdavid/CellaRepertorium
Bug Reports https://github.com/amcdavid/CellaRepertorium/issues
See More
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_1.11.0.tar.gz
Windows Binary CellaRepertorium_1.11.0.zip
macOS Binary (x86_64) CellaRepertorium_1.11.0.tgz
macOS Binary (arm64) CellaRepertorium_1.11.0.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