Package: valr 0.8.3.9000

Kent Riemondy

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], Kent Riemondy [aut, cre], RNA Bioscience Initiative [fnd, cph]

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valr/json (API)
NEWS

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

Peer review:

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

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

Uses libs:
  • c++– GNU Standard C++ Library v3

On CRAN:

bedtoolsgenomeinterval-arithmeticcpp

9.50 score 89 stars 229 scripts 588 downloads 4 mentions 50 exports 65 dependencies

Last updated 8 days agofrom:5c23a5543b. Checks:9 OK. Indexed: yes.

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R-4.4-win-x86_64OKJan 11 2025
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R-4.4-mac-aarch64OKJan 11 2025
R-4.3-win-x86_64OKJan 11 2025
R-4.3-mac-x86_64OKJan 11 2025
R-4.3-mac-aarch64OKJan 11 2025

Exports:bed_absdistbed_closestbed_clusterbed_complementbed_coveragebed_fisherbed_flankbed_genomecovbed_glyphbed_intersectbed_jaccardbed_makewindowsbed_mapbed_mergebed_partitionbed_projectionbed_randombed_reldistbed_shiftbed_shufflebed_slopbed_sortbed_subtractbed_windowbed12_to_exonsbound_intervalscheck_genomecheck_intervalconcatcreate_intronscreate_tsscreate_utrs3create_utrs5db_ensembldb_ucscflip_strandsgr_to_bedinterval_spacingread_bedread_bed12read_bedgraphread_bigwigread_broadpeakread_genomeread_gtfread_narrowpeakread_vcfvalr_examplevaluesvalues_unique

Dependencies:askpassbackportsBiocGenericsbitbit64broomclicliprcolorspacecpp11cpp11bigwigcrayoncurldplyrfansifarvergenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesggplot2gluegtablehmshttrIRangesisobandjsonlitelabelinglatticelifecyclemagrittrMASSMatrixmgcvmimemunsellnlmeopensslpillarpkgconfigprettyunitsprogresspurrrR6RColorBrewerRcppreadrrlangS4VectorsscalesstringistringrsystibbletidyrtidyselecttzdbUCSC.utilsutf8vctrsviridisLitevroomwithrXVector

valr overview

Rendered fromvalr.Rmdusingknitr::rmarkdownon Jan 11 2025.

Last update: 2023-10-11
Started: 2016-05-05

Readme and manuals

Help Manual

Help pageTopics
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 genomebed_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 intervalsbed_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 tibblegr_to_bed
Calculate interval spacing.interval_spacing
Bed-like data.frame requirements for valr functionscheck_genome check_interval genome_df ivl_df
Read BED and related files.read_bed read_bed12 read_bedgraph read_broadpeak read_narrowpeak
Read a bigwig file into a valr compatible tblread_bigwig
Read genome files.read_genome
Import and convert a GTF/GFF file into a valr compatible bed tbl formatread_gtf
Read a VCF file.read_vcf
valr: genome interval arithmetic in Rvalr-package valr
Provide working directory for valr example files.valr_example