Package: valr 0.8.2.9000

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'))

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

Uses libs:

c++– GNU Standard C++ Library v3

On CRAN:

bedtools genome interval-arithmetic

9.30 score 88 stars 233 scripts 696 downloads 4 mentions 50 exports 93 dependencies

Last updated 1 months agofrom:59b22d346d. Checks:OK: 9. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Nov 12 2024
R-4.5-win-x86_64	OK	Nov 12 2024
R-4.5-linux-x86_64	OK	Nov 12 2024
R-4.4-win-x86_64	OK	Nov 12 2024
R-4.4-mac-x86_64	OK	Nov 12 2024
R-4.4-mac-aarch64	OK	Nov 12 2024
R-4.3-win-x86_64	OK	Nov 12 2024
R-4.3-mac-x86_64	OK	Nov 12 2024
R-4.3-mac-aarch64	OK	Oct 13 2024

Exports: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 db_ensembl db_ucsc flip_strands gr_to_bed interval_spacing read_bed read_bed12 read_bedgraph read_bigwig read_broadpeak read_genome read_gtf read_narrowpeak read_vcf valr_example values values_unique

Dependencies:abind askpass backports BH Biobase BiocGenerics BiocIO BiocParallel Biostrings bit bit64 bitops broom cli clipr codetools colorspace cpp11 crayon curl DelayedArray dplyr fansi farver formatR futile.logger futile.options generics GenomeInfoDb GenomeInfoDbData GenomicAlignments GenomicRanges ggplot2 glue gtable hms httr IRanges isoband jsonlite labeling lambda.r lattice lifecycle magrittr MASS Matrix MatrixGenerics matrixStats mgcv mime munsell nlme openssl pillar pkgconfig prettyunits progress purrr R6 RColorBrewer Rcpp RCurl readr restfulr Rhtslib rjson rlang Rsamtools rtracklayer S4Arrays S4Vectors scales snow SparseArray stringi stringr SummarizedExperiment sys tibble tidyr tidyselect tzdb UCSC.utils utf8 vctrs viridisLite vroom withr XML XVector yaml zlibbioc

valr overview

Rendered fromvalr.Rmdusingknitr::rmarkdownon Nov 12 2024.

Last update: 2023-10-11
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
Import and convert a bigwig file into a valr compatible tbl	read_bigwig
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-package valr
Provide working directory for valr example files.	valr_example