Package: valr 0.10.0

Jay Hesselberth

valr: Genome Interval Arithmetic

Read and manipulate genome intervals and signals. Provides functionality similar to command-line tool suites within R, enabling interactive analysis and visualization of genome-scale data. Riemondy et al. (2017) <doi:10.12688/f1000research.11997.1>.

Authors:Jay Hesselberth [aut, cre], Kent Riemondy [aut], RNA Bioscience Initiative [fnd, cph]

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manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
valr/json (API)

# Install 'valr' in R:

install.packages('valr', repos = c('https://rnabioco.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/rnabioco/valr/issues

Pkgdown/docs site:https://rnabioco.github.io

Uses libs:

c++– GNU Standard C++ Library v3

On CRAN:

bedtools genome interval-arithmetic cpp

11.05 score 95 stars 2 packages 414 scripts 3.7k downloads 4 mentions 56 exports 47 dependencies

Last updated from:9db34b7522. Checks:13 OK. Indexed: yes.

Target	Result	Time
linux-devel-arm64	OK	262
linux-devel-x86_64	OK	270
source / vignettes	OK	271
linux-release-arm64	OK	271
linux-release-x86_64	OK	269
macos-release-arm64	OK	189
macos-release-x86_64	OK	486
macos-oldrel-arm64	OK	206
macos-oldrel-x86_64	OK	404
windows-devel	OK	262
windows-release	OK	239
windows-oldrel	OK	211
wasm-release	OK	190

Exports:as_data_frame as_tibble bed_absdist bed_closest bed_cluster bed_complement bed_coverage bed_fisher bed_flank bed_genomecov bed_glyph bed_intersect bed_jaccard bed_makewindows bed_map bed_merge bed_partition bed_projection bed_random bed_reldist bed_shift bed_shuffle bed_slop bed_sort bed_subtract bed_window bed12_to_exons bound_intervals check_genome check_interval concat create_introns create_tss create_utrs3 create_utrs5 data_frame db_ensembl db_ucsc flip_strands gr_to_bed interval_spacing read_bed read_bed12 read_bedgraph read_bigbed read_bigwig read_broadpeak read_genome read_gtf read_narrowpeak read_vcf tibble tribble valr_example values values_unique

Dependencies:backports BiocGenerics bit bit64 broom cli clipr cpp11 cpp11bigwig crayon dplyr farver generics GenomicRanges ggplot2 glue gtable hms IRanges isoband labeling lifecycle magrittr pillar pkgconfig prettyunits progress purrr R6 RColorBrewer readr rlang S4Vectors S7 scales Seqinfo stringi stringr tibble tidyr tidyselect tzdb utf8 vctrs viridisLite vroom withr

valr overview

Rendered fromvalr.Rmdusingknitr::rmarkdown

Last update: 2026-06-23
Started: 2016-05-05

Citation

Development and contributors

Readme and manuals

Help Manual

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