Congratulations on your installation of CellaRepertorium. This package contains methods for manipulating, clustering, pairing, testing and conducting multimodal analysis single cell RepSeq data, especially as generated by 10X Genomics Chromium Immune Profiling.

1 Ethos and data 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 may generate multiple contigs.

Contigs belong to cells, and can also belong to a cluster. A ContigCellDB() object tracks these two types of membership by using 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.