Toolbox for Functional Genomics Data Processing in R

bam2coverage | Convert a bam file to coverage |

bed2dyad | Convert a bed file to nucleosome dyad coverage |

bin.matrix | Bin a matrix column-wise and average the bins across rows |

bin.matrix.rows | Bin a matrix column-wise per row |

convertToColors | Convert numeric matrix to colors |

coverageWindowsCenteredStranded | Get windowed strand-oriented coverages around center points |

coverageWindowsCenteredStrandedParallel | Get windowed strand-oriented coverages around center point,... |

coverageWindowsStranded | Get windowed strand-oriented coverages |

coverageWindowsStrandedParallel | Get windowed strand-oriented coverages, parallelized |

cumPlot | Cumulative plot with interquartile ranges |

meanScale | Row-wise mean scaling |

norm.square | Row-wise sum of squares normalization of a matrix |

norm.sum | Row-wise sum of row normalization of a matrix |

ocampo | Get ocampo paramters per instance |

plotProfiles | Plot coverages along genome |

plotRasterHeatmap | Plot Raster Heatmap of matrix |

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