calc_mappability |
A function to calculate the mappabilities of each NGS sample. |

Evers_CRISPRn_RT112 |
A benchmark CRISPRn pooled screen data from Evers et al. |

fit_ab |
A C++ function to perform a parameter estimation for the sgRNA-level test. It will estimate two different parameters 'phat' and 'vhat,' and we assume input count data follows the beta-binomial distribution. Dr. Keith Baggerly initially implemented this code in Matlab, and it has been rewritten it in C++ for the speed-up. |

get_CPM |
A function to normalize sgRNA read counts. |

join_count_and_design |
A function to join a count table and a design table. |

measure_gene_stats |
A function to perform gene-level test using a sgRNA-level statistics. |

measure_sgrna_stats |
A function to perform a statistical test at a sgRNA-level |

plot_corr_heatmap |
A function to show a heatmap sgRNA-level corrleations of the NGS samples. |

plot_count_distribution |
A function to plot read count distribution. |

plot_dotplot |
A function to visualize dot plots for a gene. |

plot_PCA |
A function to plot the first two principal components of samples. |

quant |
A C++ function to quantify sgRNA abundance from NGS samples. |

run_estimation |
A function to perform a statistical test at a sgRNA-level, deprecated. |

run_sgrna_quant |
A function to run a sgRNA quantification algorithm from NGS sample |

Sanson_CRISPRn_A375 |
A benchmark CRISPRn pooled screen data from Sanson et al. |