DOI: 10.18129/B9.bioc.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>

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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


biocViews Clustering, ImmunoOncology, RNASeq, SingleCell, Software, TargetedResequencing, Technology, Transcriptomics
Version 1.13.0
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
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Suggests testthat, readr, knitr, rmarkdown, ggplot2, BiocStyle, ggdendro, broom, lme4, RColorBrewer, SingleCellExperiment, scater, broom.mixed, cowplot, igraph, ggraph
URL https://github.com/amcdavid/CellaRepertorium
BugReports https://github.com/amcdavid/CellaRepertorium/issues
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