# Data structures, clustering and testing for single cell immune receptor repertoires (scRNAseq RepSeq/AIRR-seq)

## Documentation for package ‘CellaRepertorium’ version 1.4.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

$-method | Access public members of ContigCellDB object.
$<--method | Access public members of ContigCellDB object.
.cluster_permute_test | Cell permutation tests (internal)
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_logistic_test | Test clusters for differential usage
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
ContigCellDB | Construct a ContigCellDB
ContigCellDB-mutate | Access public members of ContigCellDB object.
ContigCellDB_10XVDJ | Construct a ContigCellDB
contigs_qc | Filtered and annotated contigs of TCR from mice
crosstab_by_celltype | Count contig UMIs by celltype
cross_tab_tbl | Generate a 2d cross tab using arbitrary numbers of columns as factors
dim-method | 'data.frame'-like mutation/accessor generics for 'ContigCellDB' objects
dimnames-method | 'data.frame'-like mutation/accessor generics for 'ContigCellDB' objects
entropy | Calculate the entropy of a vector
enumerate_pairing | Categorize the pairing present in a cell
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_clustering | Perform additional clustering of sequences within groups
fine_cluster_seqs | Calculate distances and perform hierarchical clustering on a set of sequences
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
left_join_warn | Perform a 'dplyr::left_join()' but check for non-key overlapping fields
map_axis_labels | Color axis labels
modal_category | Calculate the entropy of a vector
mutate_cdb | Create new or update existing columns of 'ContigCellDB' tables
ncol-method | 'data.frame'-like mutation/accessor generics for 'ContigCellDB' objects
np | Calculate the entropy of a vector
nrow-method | 'data.frame'-like mutation/accessor generics for 'ContigCellDB' objects
pairing_tables | Generate a list of tables representing clusters paired in cells
plot_cluster_factors | Visualization of pairs of cluster factor
plot_permute_test | Tests for independence between labels and covariates using permutation of cells
purity | Calculate number of cluster-subject singletons for the purposes of permutation testing
rank_chain_ccdb | Rank contigs, per cell, by experiment-wide prevalence of 'cluster_pk', which is added as the 'prevalence' field
rank_prevalence_ccdb | Rank contigs, per cell, by experiment-wide prevalence of 'cluster_pk', which is added as the 'prevalence' field
rbind-method | Combine 'ContigCellDB' along rows (contigs, cells or clusters).
rbind.ContigCellDB | 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
tcr_chain_recode | Categorize the pairing present in a cell
[-method | 'data.frame'-like mutation/accessor generics for 'ContigCellDB' objects
[[-method | 'data.frame'-like mutation/accessor generics for 'ContigCellDB' objects