alphabetr

alphabetr implements the ALPHABETR (algorithm for pairing alpha-beta T cell receptors) algorithms for obtaining TCR sequence pairs. This approach determines CDR3A/CDR3B pairs from high-throughput sequencing data from repeated samples of antigen-specific T cell populations.

With alphabetr, you can

• Determine CDR3A/CDR3B pairs
• Determine dual TCR-alpha clones and clones that share CDR3A or CDR3B sequences
• Estimate clonal frequencies

You can install

• the latest version released on CRAN with

install.packages("alphabetr")

• the latest development version found on github with

if (packageVersion("devtools") < 1.6) {
  install.packages("devtools")
}
# devtools::install_github("edwardslee/alphabetr")
install.packages("alphabetr", repos = c('https://edwardslee.r-universe.dev', 'https://cloud.r-project.org'))

If you encounter any bugs, please file an issue.

More information

Please see our paper in PLOS Computational Biology for more details about the algorithm and how it was tested (DOI: 10.1371/journal.pcbi.1005313).