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

bagpipe | Identify candidate alpha/beta pairs. |

chain_scores | Calculate association scores between alpha and beta chain... |

combine_freq_results | Combines the frequency estimation results from single TCR... |

create_clones | Create a synthetic set of clones with a specific underlying... |

create_data | Simulate sequencing data obtained from the alphabetr approach... |

create_data_singlecells | Simulate sequencing data obtained single-cell sequencing |

dual_discrim_dual_likelihood | Calculate likelihood of two beta-sharing candidate alpha-beta... |

dual_discrim_shared_likelihood | Calculate likelihood of two beta-sharing candidate alpha-beta... |

dual_eval | Calculate dual depths and false dual rates for simulated... |

dual_tail | Discriminate between beta-sharing clones and dual-alpha TCR... |

dual_top | Discriminate between beta-sharing clones and dual-alpha TCR... |

freq_estimate | Estimation of frequencies of clones identified by 'alphabetr' |

freq_eval | Calculate the precision, CV, and accuracy of frequency... |

likelihood_dual | Calculate likelihood curve of frequency estimates for a... |

likelihood_dualdual | Calculate likelihood curve of frequency estimates for a... |

likelihood_single | Calculate likelihood curve of frequency estimates for a... |

read_alphabetr | Read in alphabetr sequencing data into the binary matrix form... |

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