An R package for analysis of massive parallel sequencing based RNA structure probing data

bam2bedgraph | Function converts bam file to bedgraph by counting number of... |

BED2txDb | Bedgraph to TranscriptDb object |

bedgraph2norm | Import bedgraph to GRanges |

comp | Arranging information from GRanges produced by readsamples()... |

compdata | Create or extend norm_GR GRanges using Comp_GR GRanges |

correct_oversaturation | Correcting EUC of oversaturated fragments. |

dtcr | Calculate deltaTCR. |

GR2norm_df | Export normalized GRanges object to data frame |

k2n_calc | Calculate number of Estimated Unique Counts (EUC's)... |

norm2bedgraph | Exporting data in norm_df data frame (product of dtcr,... |

norm_df2GR | Function to convert norm_df data frame (product of... |

plotReads | Plotting ranges from GRanges |

plotRNA | Plot normalized values over transcript positions |

readsamples | Import of tables prepared by Galaxy workflow to R environment |

slograt | Smooth Log2-ratio |

swinsor | Smooth Winsorization |

swinsor_vector | Smooth Winsor Normalization |

winsor | Winsor normalization with fitting to <0,1> range. |

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