valr: Genome Interval Arithmetic in R

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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.

Author
Jay Hesselberth [aut, cre], Kent Riemondy [aut], Ryan Sheridan [ctb]
Date of publication
2016-12-01 11:28:13
Maintainer
Jay Hesselberth <jay.hesselberth@gmail.com>
License
MIT + file LICENSE
Version
0.1.1
URLs

View on CRAN

Man pages

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 on number of shared and unique intervals.
bed_flank
Create flanking intervals from input intervals.
bed_glyph
Create example glyphs for valr functions.
bed_intersect
Identify intersecting intervals.
bed_jaccard
Calculate jaccard statistics on 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 tbl of intervals.
bed_subtract
Subtract intervals.
bed_window
Identify intervals within a specified distance.
bound_intervals
Select intervals bounded by a genome.
db
Fetch data from remote databases.
flip_strands
Flip strands in intervals.
interval_spacing
Calculate interval spacing.
launch_shiny
launch valr shiny demo
read_bed
Read BED and related files.
read_genome
Read genome files.
read_vcf
Read a VCF file.
valr
valr: genome interval arithmetic in R
valr_example
Provide working directory for valr example files.

Files in this package

valr
valr/inst
valr/inst/CITATION
valr/inst/shiny
valr/inst/shiny/app.r
valr/inst/extdata
valr/inst/extdata/mm9.bed12.gz
valr/inst/extdata/hg19.refGene.chr22.bed.gz
valr/inst/extdata/3fields.bed.gz
valr/inst/extdata/hg19.snps147.chr22.bed.gz
valr/inst/extdata/12fields.bed.gz
valr/inst/extdata/sample.broadPeak.gz
valr/inst/extdata/sample.narrowPeak.gz
valr/inst/extdata/hg19.chrom.sizes.gz
valr/inst/extdata/test.vcf.gz
valr/inst/extdata/hg19.rmsk.chr22.bed.gz
valr/inst/extdata/hela.h3k4.chip.bg.gz
valr/inst/extdata/6fields.bed.gz
valr/inst/extdata/test.bg.gz
valr/inst/extdata/genome.txt.gz
valr/inst/extdata/genes.hg19.chr22.bed.gz
valr/inst/doc
valr/inst/doc/interval-stats.R
valr/inst/doc/valr.Rmd
valr/inst/doc/valr.html
valr/inst/doc/interval-stats.Rmd
valr/inst/doc/interval-stats.html
valr/inst/doc/valr.R
valr/inst/include
valr/inst/include/valr.h
valr/inst/include/IntervalTree.h
valr/tests
valr/tests/testthat.R
valr/tests/testthat
valr/tests/testthat/test_utils.R
valr/tests/testthat/test_merge.r
valr/tests/testthat/test_read_bed.r
valr/tests/testthat/test-db.r
valr/tests/testthat/test_bed12_to_exons.r
valr/tests/testthat/test_makewindows.r
valr/tests/testthat/test_random.r
valr/tests/testthat/test_intersect.r
valr/tests/testthat/test_glyph.r
valr/tests/testthat/test_map.r
valr/tests/testthat/test_spacing.r
valr/tests/testthat/test_sort.r
valr/tests/testthat/test_shuffle.r
valr/tests/testthat/test-style.r
valr/tests/testthat/test_absdist.r
valr/tests/testthat/test_read_vcf.r
valr/tests/testthat/test_genome.r
valr/tests/testthat/test_fisher.r
valr/tests/testthat/test_window.r
valr/tests/testthat/helper-astyle.r
valr/tests/testthat/test_closest.r
valr/tests/testthat/test_slop.r
valr/tests/testthat/test_jaccard.r
valr/tests/testthat/test_subtract.r
valr/tests/testthat/test_complement.r
valr/tests/testthat/test_projection.r
valr/tests/testthat/test_flank.r
valr/tests/testthat/test_shift.r
valr/tests/testthat/test_reldist.R
valr/tests/testthat/test_cluster.r
valr/tests/testthat/test_coverage.r
valr/tests/testthat/test_strands.r
valr/src
valr/src/reldist.cpp
valr/src/Makevars
valr/src/random.cpp
valr/src/intersect.cpp
valr/src/absdist.cpp
valr/src/coverage.cpp
valr/src/utils.cpp
valr/src/shuffle.cpp
valr/src/complement.cpp
valr/src/subtract.cpp
valr/src/Makevars.win
valr/src/RcppExports.cpp
valr/src/closest.cpp
valr/src/merge.cpp
valr/NAMESPACE
valr/NEWS.md
valr/R
valr/R/globals.r
valr/R/bed_absdist.r
valr/R/read_genome.r
valr/R/bed_sort.r
valr/R/read_bed.r
valr/R/bed_random.r
valr/R/db.r
valr/R/bed_makewindows.r
valr/R/bed_window.r
valr/R/bed_coverage.R
valr/R/strands.r
valr/R/bed_shift.r
valr/R/bed_slop.r
valr/R/bed_fisher.r
valr/R/bed_projection.r
valr/R/bed_intersect.r
valr/R/read_vcf.r
valr/R/spacing.r
valr/R/utils.r
valr/R/valr.r
valr/R/bed_merge.r
valr/R/RcppExports.R
valr/R/bed12_to_exons.r
valr/R/bed_reldist.r
valr/R/bed_jaccard.r
valr/R/bed_subtract.r
valr/R/bed_closest.r
valr/R/bed_glyph.r
valr/R/bed_complement.r
valr/R/launch_shiny.r
valr/R/bed_cluster.r
valr/R/bed_map.r
valr/R/bed_flank.r
valr/R/bed_shuffle.r
valr/vignettes
valr/vignettes/valr.Rmd
valr/vignettes/interval-stats.Rmd
valr/README.md
valr/MD5
valr/build
valr/build/vignette.rds
valr/DESCRIPTION
valr/man
valr/man/bed_coverage.Rd
valr/man/bed_cluster.Rd
valr/man/bed_slop.Rd
valr/man/bed_intersect.Rd
valr/man/bed_shift.Rd
valr/man/interval_spacing.Rd
valr/man/bed_complement.Rd
valr/man/bed_sort.Rd
valr/man/bed_subtract.Rd
valr/man/db.Rd
valr/man/bed_projection.Rd
valr/man/valr.Rd
valr/man/bed_makewindows.Rd
valr/man/bed_fisher.Rd
valr/man/read_genome.Rd
valr/man/bed_merge.Rd
valr/man/read_bed.Rd
valr/man/bed_shuffle.Rd
valr/man/launch_shiny.Rd
valr/man/bed_window.Rd
valr/man/bed_map.Rd
valr/man/bed_reldist.Rd
valr/man/bed_flank.Rd
valr/man/bed12_to_exons.Rd
valr/man/bed_random.Rd
valr/man/bed_jaccard.Rd
valr/man/flip_strands.Rd
valr/man/bed_glyph.Rd
valr/man/bed_closest.Rd
valr/man/bed_absdist.Rd
valr/man/valr_example.Rd
valr/man/read_vcf.Rd
valr/man/bound_intervals.Rd
valr/LICENSE