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() |