Function reference • CellaRepertorium

Constuction and modification Functions to construct and modify a ContigCellDB
`ContigCellDB()` `ContigCellDB_10XVDJ()`	Construct a ContigCellDB
`$`(<ContigCellDB>) `$<-`(<ContigCellDB>)	Access public members of ContigCellDB object.
`filter_cdb()` `mutate_cdb()`	Create new or update existing columns of `ContigCellDB` tables
`rbind(<ContigCellDB>)`	Combine `ContigCellDB` along rows (contigs, cells or clusters).
`split_cdb()`	Split into a list of `ContigCellDB()` by named fields
`equalize_ccdb()`	Take the intersection of keys in tables in `x`
Interfacing with mRNA-based SingleCellExperiment objects Merging and joint analysis of ContigCellDB and SingleCellExperiment
`ccdb_join()`	Join dataframe or SingleCellExperiment object with ContigCellDB object
Clustering Methods to cluster contigs
`cluster_germline()`	Cluster contigs by germline properties
`fine_clustering()`	Perform additional clustering of sequences within groups
`cdhit_ccdb()`	Use `cdhit()` to cluster a `ContigCellDB()`
`pairing_tables()`	Generate a list of tables representing clusters paired in cells
`cluster_filterset()`	A filtration of clusters
Canonicalization Methods to return single contigs for cells or clusters
`crosstab_by_celltype()`	Count contig UMIs by celltype
`guess_celltype()`	Guess the cell type of a contig from the chain ID
`canonicalize_cell()`	Find a canonical contig to represent a cell
`canonicalize_cluster()`	Find a canonical contig to represent a cluster
`ig_chain_recode()` `tcr_chain_recode()` `enumerate_pairing()`	Categorize the pairing present in a cell
Statistical testing
`cluster_permute_test()`	Tests for independence between labels and covariates using permutation of cells
`cluster_test_by()` `cluster_logistic_test()`	Test clusters for differential usage
`purity()`	Calculate number of cluster-subject singletons for the purposes of permutation testing
Plotting
`map_axis_labels()`	Color axis labels
Datasets
`ccdb_ex`	A preconstructed `ContigClusterDB` from the `contigs_qc` data
`contigs_qc`	Filtered and annotated contigs of TCR from mice
Internal or WIP Functions that may be made internal, removed, or with interfaces subject to change.
`.cluster_permute_test()`	Cell permutation tests (internal)
`entropy()` `np()` `modal_category()`	Calculate the entropy of a vector
`fancy_name_contigs()`	Generate a legible name for a series of contigs
`fine_cluster_seqs()`	Calculate distances and perform hierarchical clustering on a set of sequences

Reference

Constuction and modification

Interfacing with mRNA-based SingleCellExperiment objects

Clustering

Canonicalization

Statistical testing

Plotting

Datasets

Internal or WIP