kmerPyramid: an interactive visualization tool for nucleobase and \textit{k}-mer frequencies

bacteriaKmerDistribution | k-mer distribution of bacteria DNA sequences |

generate_paired_reads | Generate paired reads from a given genome |

get_diff_values | Get the difference in counts between to sequences |

get_kmer_distribution | Get the k-mer distribution from a sequence |

get_pca_plot_list | Calculate the PCA with pyramid edges |

get_pca_window_list | Get the PCA values for sliding window |

get_reads_num | Calculate number of reads given the coverage and genome size |

get_window_distr | Wrapper for the sliding window k-mer distribution |

pyramid_3d | ACGT pyramid 3D ploting function |

pyramid_3d_draw_edges | Function to draw the edges of the 3D pyramid |

pyramid_3d_grid | The k-mer grid pyramid 3D plotting function |

read.fastq | Function to read in fastq files |

translate.phred | Test title for later |

viralExampleCodingSeq | DNAStringSet of coding and non coding of NC_015230.1 viral... |

viralExampleSeqs | DNAStringSet of ten viral sequences |

virusKmerDistribution | k-mer distribution of virus DNA sequences |

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