R: Algorithms for High-Throughput Sequencing of Antigen-Specific T Cells

# Algorithms for High-Throughput Sequencing of Antigen-Specific T Cells

## Documentation for package ‘alphabetr’ version 0.2.2

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

## Help Pages

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()