CellaRepertorium
This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see CellaRepertorium.
Data structures, clustering and testing for single cell immune receptor repertoires (scRNAseq RepSeq/AIRR-seq)
Bioconductor version: 3.16
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("CellaRepertorium")):
Installation
To install this package, start R (version "4.2") and enter:
if (!require("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")| 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 | ||
| NEWS | Text |
Details
| biocViews | Clustering, ImmunoOncology, RNASeq, SingleCell, Software, TargetedResequencing, Technology, Transcriptomics |
| Version | 1.8.0 |
| 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_1.8.0.tar.gz |
| Windows Binary | CellaRepertorium_1.8.0.zip (64-bit only) |
| macOS Binary (x86_64) | CellaRepertorium_1.8.0.tgz |
| macOS Binary (arm64) | CellaRepertorium_1.8.0.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 |
| Old Source Packages for BioC 3.16 | Source Archive |