Algorithms for High-Throughput Sequencing of Antigen-Specific T Cells
Identify candidate alpha/beta pairs.
Calculate association scores between alpha and beta chain pairs.
Combines the frequency estimation results from single TCR clones and d...
Create a synthetic set of clones with a specific underlying clonal str...
Simulate sequencing data obtained from the alphabetr approach with a s...
Simulate sequencing data obtained single-cell sequencing
Calculate likelihood of two beta-sharing candidate alpha-beta pairs de...
Calculate likelihood of two beta-sharing candidate alpha-beta pairs de...
Calculate dual depths and false dual rates for simulated alphabetr exp...
Discriminate between beta-sharing clones and dual-alpha TCR clones (op...
Discriminate between beta-sharing clones and dual-alpha TCR clones (op...
Estimation of frequencies of clones identified by alphabetr
Calculate the precision, CV, and accuracy of frequency estimates
Calculate likelihood curve of frequency estimates for a dual-alpha or ...
Calculate likelihood curve of frequency estimates for a dual-alpha and...
Calculate likelihood curve of frequency estimates for a single TCR clo...
Read in alphabetr sequencing data into the binary matrix form needed b...
Provides algorithms for frequency-based pairing of alpha-beta T cell receptors.