Genome Interval Arithmetic in R

as.tbl_genome | Coerce objects to tbl_genome. |

as.tbl_interval | Coerce objects to tbl_intervals. |

bed12_to_exons | Convert BED12 to individual exons in BED6. |

bed_absdist | Compute absolute distances between intervals. |

bed_closest | Identify closest intervals. |

bed_cluster | Cluster neighboring intervals. |

bed_complement | Identify intervals in a genome not covered by a query. |

bed_coverage | Compute coverage of intervals. |

bed_fisher | Fisher's test to measure overlap between two sets of... |

bed_flank | Create flanking intervals from input intervals. |

bed_glyph | Create example glyphs for valr functions. |

bed_intersect | Identify intersecting intervals. |

bed_jaccard | Calculate the Jaccard statistic for two sets of intervals. |

bed_makewindows | Divide intervals into new sub-intervals ("windows"). |

bed_map | Calculate summaries and statistics from overlapping... |

bed_merge | Merge overlapping intervals. |

bed_projection | Projection test for query interval overlap. |

bed_random | Generate randomly placed intervals on a genome. |

bed_reldist | Compute relative distances between intervals. |

bed_shift | Adjust intervals by a fixed size. |

bed_shuffle | Shuffle input intervals. |

bed_slop | Increase the size of input intervals. |

bed_sort | Sort a set of intervals. |

bed_subtract | Subtract two sets of intervals. |

bed_window | Identify intervals within a specified distance. |

bound_intervals | Select intervals bounded by a genome. |

create_introns | Create intron features. |

create_tss | Create transcription start site features. |

create_utrs3 | Create 3' UTR features. |

create_utrs5 | Create 5' UTR features. |

db | Fetch data from remote databases. |

flip_strands | Flip strands in intervals. |

interval_spacing | Calculate interval spacing. |

is.tbl_genome | Test if the object is a tbl_genome. |

is.tbl_interval | Test if the object is a tbl_interval. |

read_bed | Read BED and related files. |

read_genome | Read genome files. |

read_vcf | Read a VCF file. |

tbl_genome | Tibble for reference sizes. |

tbl_interval | Tibble for intervals. |

valr | valr: genome interval arithmetic in R |

valr_example | Provide working directory for valr example files. |

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