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

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.

Package details

AuthorAndrew McDavid [aut, cre], Yu Gu [aut], Erik VonKaenel [aut], Thomas Lin Pedersen [ctb]
Bioconductor views Clustering ImmunoOncology RNASeq SingleCell TargetedResequencing Technology Transcriptomics
MaintainerAndrew McDavid <Andrew_McDavid@urmc.rochester.edu>
URL https://github.com/amcdavid/CellaRepertorium
Package repositoryView on Bioconductor
Installation Install the latest version of this package by entering the following in R:
if (!requireNamespace("BiocManager", quietly = TRUE))


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CellaRepertorium documentation built on Nov. 8, 2020, 7:48 p.m.