Package index
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read_bed()
read_bed12()
read_bedgraph()
read_narrowpeak()
read_broadpeak()
- Read BED and related files.
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read_bigwig()
- Import and convert a bigwig file into a valr compatible tbl
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read_genome()
- Read genome files.
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read_gtf()
- Import and convert a GTF/GFF file into a valr compatible bed tbl format
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read_vcf()
- Read a VCF file.
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db_ucsc()
db_ensembl()
- Fetch data from remote databases.
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bed_cluster()
- Cluster neighboring intervals.
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bed_complement()
- Identify intervals in a genome not covered by a query.
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bed_flank()
- Create flanking intervals from input intervals.
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bed_genomecov()
- Calculate coverage across a genome
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bed_merge()
- Merge overlapping intervals.
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bed_partition()
- Partition intervals into elemental intervals
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bed_slop()
- Increase the size of input intervals.
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bed_shift()
- Adjust intervals by a fixed size.
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bed_sort()
- Sort a set of intervals.
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bed_closest()
- Identify closest intervals.
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bed_coverage()
- Compute coverage of intervals.
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bed_intersect()
- Identify intersecting intervals.
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bed_map()
concat()
values_unique()
values()
- Calculate summaries from overlapping intervals.
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bed_subtract()
- Subtract two sets of intervals.
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bed_window()
- Identify intervals within a specified distance.
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bed_random()
- Generate randomly placed intervals on a genome.
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bed_shuffle()
- Shuffle input intervals.
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bed_absdist()
- Compute absolute distances between intervals.
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bed_reldist()
- Compute relative distances between intervals.
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bed_fisher()
- Fisher's test to measure overlap between two sets of intervals.
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bed_jaccard()
- Calculate the Jaccard statistic for two sets of intervals.
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bed_projection()
- Projection test for query interval overlap.
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create_introns()
- Create intron features.
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create_tss()
- Create transcription start site features.
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create_utrs3()
- Create 3' UTR features.
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create_utrs5()
- Create 5' UTR features.
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bed_makewindows()
- Divide intervals into new sub-intervals ("windows").
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bed12_to_exons()
- Convert BED12 to individual exons in BED6.
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bed_glyph()
- Create example glyphs for valr functions.
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bound_intervals()
- Select intervals bounded by a genome.
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flip_strands()
- Flip strands in intervals.
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gr_to_bed()
- Convert Granges to bed tibble
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interval_spacing()
- Calculate interval spacing.
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check_interval()
check_genome()
- Bed-like data.frame requirements for valr functions
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valr-package
valr
- valr: genome interval arithmetic in R
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valr_example()
- Provide working directory for valr example files.