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.
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.
#> Warning in knitr::include_graphics(system.file("help/figures/ #> contig_schematic.png", : It is highly recommended to use relative paths #> for images. You had absolute paths: "/tmp/RtmpvcwGGM/Rinst2b9cd778e31de5/ #> CellaRepertorium/help/figures/contig_schematic.png"
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
tracks columns (the primary keys) that uniquely identify each row in
each of these tables. The
contig_tbl is the
cell_tbl contains the cells, and the
cluster_tbl contains the clusters.
#> Warning in knitr::include_graphics(system.file("help/figures/ #> table_schematic.png", : It is highly recommended to use relative paths #> for images. You had absolute paths: "/tmp/RtmpvcwGGM/Rinst2b9cd778e31de5/ #> CellaRepertorium/help/figures/table_schematic.png"