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