$,ContigCellDB-method   Access public members of ContigCellDB object.
.cluster_permute_test   Cell permutation tests (internal)
ContigCellDB            Construct a ContigCellDB
[[,ContigCellDB,character,missing-method
                        'data.frame'-like mutation/accessor generics
                        for 'ContigCellDB' objects
canonicalize_cell       Find a canonical contig to represent a cell
canonicalize_cluster    Find a canonical contig to represent a cluster
ccdb_ex                 A preconstructed 'ContigClusterDB' from the
                        'contigs_qc' data
ccdb_join               Join dataframe or SingleCellExperiment object
                        with ContigCellDB object
cdhit                   R interface to CDHIT/CDHITest
cdhit_ccdb              Use 'cdhit()' to cluster a 'ContigCellDB()'
cland                   Cluster "And" intersection
cluster_filterset       A filtration of clusters
cluster_germline        Cluster contigs by germline properties
cluster_permute_test    Tests for independence between labels and
                        covariates using permutation of cells
cluster_plot            Make a plot showing properties of the
                        clustering
cluster_test_by         Test clusters for differential usage
contigs_qc              Filtered and annotated contigs of TCR from mice
cross_tab_tbl           Generate a 2d cross tab using arbitrary numbers
                        of columns as factors
crosstab_by_celltype    Count contig UMIs by celltype
entropy                 Calculate the entropy of a vector
equalize_ccdb           Take the intersection of keys in tables in 'x'
fancy_name_contigs      Generate a legible name for a series of contigs
filter_cdb              Create new or update existing columns of
                        'ContigCellDB' tables
fine_cluster_seqs       Calculate distances and perform hierarchical
                        clustering on a set of sequences
fine_clustering         Perform additional clustering of sequences
                        within groups
generate_pseudobulk     Generate "pseudobulk" data from a
                        'ContigCellDB'
guess_celltype          Guess the cell type of a contig from the chain
                        ID
hushWarning             Selectively muffle warnings based on output
ig_chain_recode         Categorize the pairing present in a cell
map_axis_labels         Color axis labels
pairing_tables          Generate a list of tables representing clusters
                        paired in cells
plot_cluster_factors    Visualization of pairs of cluster factor
purity                  Calculate number of cluster-subject singletons
                        for the purposes of permutation testing
rank_prevalence_ccdb    Rank contigs, per cell, by experiment-wide
                        prevalence of 'cluster_pk', which is added as
                        the 'prevalence' field
rbind,ContigCellDB-method
                        Combine 'ContigCellDB' along rows (contigs,
                        cells or clusters).
right_join_warn         Perform a 'dplyr::left_join()' but check for
                        non-key overlapping fields
split_cdb               Split into a list of 'ContigCellDB()' by named
                        fields
