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CellaRepertorium

R-CMD-check

This package contains methods for clustering, pairing and testing single cell RepSeq data, especially as generated by 10X genomics VDJ solution.

Installation

Install with

install.packages('BiocManager') # if you don't have it yet
BiocManager::version() # Check that Bioconductor version >= 3.12 
BiocManager::valid() # And it's in a sane state.
BiocManager::install('CellaRepertorium') # install

For the development version, install via devtools::install_github('amcdavid/CellaRepertorium').

Data requirements and package structure

The fundamental unit this package operates on is the contig, which is a section of contiguously stitched reads from a single cell. Each contig belongs to one (and only one) cell, however, cells generate multiple contigs.

Contigs can also belong to a cluster. Because of these two many-to-one mappings, these data can be thought as a series of ragged arrays. The links between them mean they are relational data. A ContigCellDB() object wraps each of these objects as a sequence of three data.frames (dplyr::tibble(), actually). ContigCellDB() also tracks columns (the primary keys) that uniquely identify each row in each of these tables. The contig_tbl is the tibble containing contigs, the cell_tbl contains the cells, and the cluster_tbl contains the clusters.

The contig_pk, cell_pk and cluster_pk specify the columns that identify a contig, cell and cluster, respectively. These will serve as foreign keys that link the three tables together. The tables are kept in sync so that subsetting the contigs will subset the cells, and clusters, and vice-versa.

Of course, each of these tables can contain many other columns that will serve as covariates for various analyses, such as the CDR3 sequence, or the identity of the V, D and J regions. Various derived quantities that describe cells and clusters can also be calculated, and added to these tables, such as the medoid of a cluster – a contig that minimizes the average distance to all other clusters.

Some functions of interest

Mainly, this package seeks to enforce proper schema of single cell repertoire data and stay out the user’s way for various summaries they might conduct.

However, there are a variety of specialized functions, as well:

  • cdhit_ccdb(): An R interface to CDhit, which was originally ported by Thomas Lin Pedersen.
  • fine_clustering(): clustering CDR3 by edit distances (possibly using empirical amino acid substitution matrices)
  • canonicalize_cell(): Return a single contig for each cell, e.g., for combining VDJ information with 5’-based single cell expression
  • ccdb_join(): join a ccdb object from this package to a SingleCellExperiment object, by droplet barcode.
  • cluster_permute_test(): permutation tests of cluster statistics
  • cluster_logistic_test(): logistic regression tests for overrepresentation of clusters among cells
  • pairing_tables(): Generate pairings of contigs within each cell in a way that they can be plotted

Interfacing related packages for clonal analyses

  • To combine repertoire information with expression of endogenous mRNAs, this package has been used with SingleCellExperiment::SingleCellExperiment() and Seurat after generating cell canonicalizations.
  • Many tools from the Immcantation suite can work directly on ContigCellDB() objects.

Acknowledgments

Development of CellaRepertorium was funded in part by UL1 TR002001 (PI Bennet/Zand) pilot to Andrew McDavid.