bagpipe                 Identify candidate alpha/beta pairs.
chain_scores            Calculate association scores between alpha and
                        beta chain pairs.
combine_freq_results    Combines the frequency estimation results from
                        single TCR clones and dual TCR clones
create_clones           Create a synthetic set of clones with a
                        specific underlying clonal structure
create_data             Simulate sequencing data obtained from the
                        alphabetr approach with a specified clonal
                        structure
create_data_singlecells
                        Simulate sequencing data obtained single-cell
                        sequencing
dual_discrim_dual_likelihood
                        Calculate likelihood of two beta-sharing
                        candidate alpha-beta pairs deriving from a dual
                        clone
dual_discrim_shared_likelihood
                        Calculate likelihood of two beta-sharing
                        candidate alpha-beta pairs deriving from a dual
                        clone
dual_eval               Calculate dual depths and false dual rates for
                        simulated alphabetr experiments
dual_tail               Discriminate between beta-sharing clones and
                        dual-alpha TCR clones (optimized for rare
                        clones)
dual_top                Discriminate between beta-sharing clones and
                        dual-alpha TCR clones (optimized for common
                        clones)
freq_estimate           Estimation of frequencies of clones identified
                        by 'alphabetr'
freq_eval               Calculate the precision, CV, and accuracy of
                        frequency estimates
likelihood_dual         Calculate likelihood curve of frequency
                        estimates for a dual-alpha or dual-beta TCR
                        clone
likelihood_dualdual     Calculate likelihood curve of frequency
                        estimates for a dual-alpha and dual-beta TCR
                        clone
likelihood_single       Calculate likelihood curve of frequency
                        estimates for a single TCR clone
read_alphabetr          Read in alphabetr sequencing data into the
                        binary matrix form needed by bagpipe()
