HelloRanges: Introduce *Ranges to bedtools users

Translates bedtools command-line invocations to R code calling functions from the Bioconductor *Ranges infrastructure. This is intended to educate novice Bioconductor users and to compare the syntax and semantics of the two frameworks.

Author
Michael Lawrence
Date of publication
None
Maintainer
Michael Lawrence <michafla@gene.com>
License
GPL (>= 2)
Version
1.0.0

View on Bioconductor

Man pages

argparse
Argument parsing details
bedtools_closest
bedtools_closest
bedtools_complement
bedtools_complement
bedtools_coverage
bedtools_coverage
bedtools_flank
bedtools_flank
bedtools_genomecov
bedtools_genomecov
bedtools_getfasta
bedtools_getfasta
bedtools_groupby
bedtools_groupby
bedtools_intersect
bedtools_intersect
bedtools_jaccard
bedtools_jaccard
bedtools_makewindows
bedtools_makewindows
bedtools_map
bedtools_map
bedtools_merge
bedtools_merge
bedtools_multiinter
bedtools_multiinter
bedtools_nuc
bedtools_nuc
bedtools_shift
bedtools_shift
bedtools_slop
bedtools_slop
bedtools_subtract
bedtools_subtract
bedtools_unionbedg
bedtools_unionbedg
distmode
Compute the mode of a distribution
pair
Pair up two vectors

Files in this package

HelloRanges/DESCRIPTION
HelloRanges/NAMESPACE
HelloRanges/R
HelloRanges/R/a.R
HelloRanges/R/closest.R
HelloRanges/R/complement.R
HelloRanges/R/coverage.R
HelloRanges/R/flank.R
HelloRanges/R/genomecov.R
HelloRanges/R/getfasta.R
HelloRanges/R/groupby.R
HelloRanges/R/intersect.R
HelloRanges/R/jaccard.R
HelloRanges/R/makewindows.R
HelloRanges/R/map.R
HelloRanges/R/merge.R
HelloRanges/R/multiinter.R
HelloRanges/R/nuc.R
HelloRanges/R/shift.R
HelloRanges/R/slop.R
HelloRanges/R/subtract.R
HelloRanges/R/test_HelloRanges_package.R
HelloRanges/R/unionbedg.R
HelloRanges/R/utils.R
HelloRanges/build
HelloRanges/build/vignette.rds
HelloRanges/inst
HelloRanges/inst/NEWS
HelloRanges/inst/doc
HelloRanges/inst/doc/tutorial.R
HelloRanges/inst/doc/tutorial.Rnw
HelloRanges/inst/doc/tutorial.pdf
HelloRanges/inst/unitTests
HelloRanges/inst/unitTests/data
HelloRanges/inst/unitTests/data/closest
HelloRanges/inst/unitTests/data/closest/a.bed
HelloRanges/inst/unitTests/data/closest/b.bed
HelloRanges/inst/unitTests/data/closest/close-a.bed
HelloRanges/inst/unitTests/data/closest/close-b.bed
HelloRanges/inst/unitTests/data/closest/d.bed
HelloRanges/inst/unitTests/data/closest/d_id.bed
HelloRanges/inst/unitTests/data/closest/d_iu.bed
HelloRanges/inst/unitTests/data/closest/mdb1.bed
HelloRanges/inst/unitTests/data/closest/mdb2.bed
HelloRanges/inst/unitTests/data/closest/mdb3.bed
HelloRanges/inst/unitTests/data/closest/mq1.bed
HelloRanges/inst/unitTests/data/closest/strand-test-a.bed
HelloRanges/inst/unitTests/data/closest/strand-test-b.bed
HelloRanges/inst/unitTests/data/coverage
HelloRanges/inst/unitTests/data/coverage/a.bed
HelloRanges/inst/unitTests/data/coverage/b.bed
HelloRanges/inst/unitTests/data/coverage/test.genome
HelloRanges/inst/unitTests/data/flank
HelloRanges/inst/unitTests/data/flank/a.bed
HelloRanges/inst/unitTests/data/flank/tiny.genome
HelloRanges/inst/unitTests/data/genomecov
HelloRanges/inst/unitTests/data/genomecov/chip.sam
HelloRanges/inst/unitTests/data/genomecov/pair-chip.sam
HelloRanges/inst/unitTests/data/genomecov/sam-w-del.sam
HelloRanges/inst/unitTests/data/genomecov/test.genome
HelloRanges/inst/unitTests/data/genomecov/three_blocks.sam
HelloRanges/inst/unitTests/data/genomecov/y.bam
HelloRanges/inst/unitTests/data/genomecov/y.bed
HelloRanges/inst/unitTests/data/getfasta
HelloRanges/inst/unitTests/data/getfasta/blocks.bed
HelloRanges/inst/unitTests/data/getfasta/t.fa
HelloRanges/inst/unitTests/data/groupby
HelloRanges/inst/unitTests/data/groupby/a_vcfSVtest.vcf
HelloRanges/inst/unitTests/data/groupby/values3.header.bed
HelloRanges/inst/unitTests/data/intersect
HelloRanges/inst/unitTests/data/intersect/a.bed
HelloRanges/inst/unitTests/data/intersect/b.bed
HelloRanges/inst/unitTests/data/intersect/c.bed
HelloRanges/inst/unitTests/data/intersect/d.bed
HelloRanges/inst/unitTests/data/intersect/one_block.sam
HelloRanges/inst/unitTests/data/intersect/three_blocks.sam
HelloRanges/inst/unitTests/data/intersect/three_blocks_match.bed
HelloRanges/inst/unitTests/data/intersect/three_blocks_match_1bp.bed
HelloRanges/inst/unitTests/data/intersect/three_blocks_nomatch.bed
HelloRanges/inst/unitTests/data/intersect/two_blocks.sam
HelloRanges/inst/unitTests/data/intersect/x.bed
HelloRanges/inst/unitTests/data/intersect/y.bed
HelloRanges/inst/unitTests/data/jaccard
HelloRanges/inst/unitTests/data/jaccard/a.bam
HelloRanges/inst/unitTests/data/jaccard/a.bed
HelloRanges/inst/unitTests/data/jaccard/aMixedStrands.bed
HelloRanges/inst/unitTests/data/jaccard/bMixedStrands.bed
HelloRanges/inst/unitTests/data/jaccard/e.bed
HelloRanges/inst/unitTests/data/jaccard/three_blocks_match.bam
HelloRanges/inst/unitTests/data/jaccard/three_blocks_match.bed
HelloRanges/inst/unitTests/data/makewindows
HelloRanges/inst/unitTests/data/makewindows/input.bed
HelloRanges/inst/unitTests/data/makewindows/test.genome
HelloRanges/inst/unitTests/data/map
HelloRanges/inst/unitTests/data/map/ivls.bed
HelloRanges/inst/unitTests/data/map/ivls2.bed
HelloRanges/inst/unitTests/data/map/test.gff2
HelloRanges/inst/unitTests/data/map/values.bed
HelloRanges/inst/unitTests/data/map/values5.bed
HelloRanges/inst/unitTests/data/merge
HelloRanges/inst/unitTests/data/merge/a.bed
HelloRanges/inst/unitTests/data/merge/a.full.bed
HelloRanges/inst/unitTests/data/merge/a.names.bed
HelloRanges/inst/unitTests/data/merge/fullFields.bam
HelloRanges/inst/unitTests/data/merge/testA.vcf
HelloRanges/inst/unitTests/data/multiinter
HelloRanges/inst/unitTests/data/multiinter/a.bed
HelloRanges/inst/unitTests/data/multiinter/b.bed
HelloRanges/inst/unitTests/data/multiinter/c.bed
HelloRanges/inst/unitTests/data/multiinter/test.genome
HelloRanges/inst/unitTests/data/nuc
HelloRanges/inst/unitTests/data/nuc/a.bed
HelloRanges/inst/unitTests/data/nuc/test.fasta
HelloRanges/inst/unitTests/data/shift
HelloRanges/inst/unitTests/data/shift/a.bed
HelloRanges/inst/unitTests/data/shift/tiny.genome
HelloRanges/inst/unitTests/data/slop
HelloRanges/inst/unitTests/data/slop/a.bed
HelloRanges/inst/unitTests/data/slop/tiny.genome
HelloRanges/inst/unitTests/data/subtract
HelloRanges/inst/unitTests/data/subtract/a.bed
HelloRanges/inst/unitTests/data/subtract/b.bed
HelloRanges/inst/unitTests/data/subtract/c.bed
HelloRanges/inst/unitTests/data/subtract/d.bed
HelloRanges/inst/unitTests/data/unionbedg
HelloRanges/inst/unitTests/data/unionbedg/a.bedGraph
HelloRanges/inst/unitTests/data/unionbedg/b.bedGraph
HelloRanges/inst/unitTests/data/unionbedg/c.bedGraph
HelloRanges/inst/unitTests/data/unionbedg/test.genome
HelloRanges/inst/unitTests/test_closest.R
HelloRanges/inst/unitTests/test_coverage.R
HelloRanges/inst/unitTests/test_flank.R
HelloRanges/inst/unitTests/test_genomecov.R
HelloRanges/inst/unitTests/test_getfasta.R
HelloRanges/inst/unitTests/test_groupby.R
HelloRanges/inst/unitTests/test_intersect.R
HelloRanges/inst/unitTests/test_jaccard.R
HelloRanges/inst/unitTests/test_makewindows.R
HelloRanges/inst/unitTests/test_map.R
HelloRanges/inst/unitTests/test_merge.R
HelloRanges/inst/unitTests/test_multiinter.R
HelloRanges/inst/unitTests/test_nuc.R
HelloRanges/inst/unitTests/test_shift.R
HelloRanges/inst/unitTests/test_slop.R
HelloRanges/inst/unitTests/test_subtract.R
HelloRanges/inst/unitTests/test_unionbedg.R
HelloRanges/man
HelloRanges/man/argparse.Rd
HelloRanges/man/bedtools_closest.Rd
HelloRanges/man/bedtools_complement.Rd
HelloRanges/man/bedtools_coverage.Rd
HelloRanges/man/bedtools_flank.Rd
HelloRanges/man/bedtools_genomecov.Rd
HelloRanges/man/bedtools_getfasta.Rd
HelloRanges/man/bedtools_groupby.Rd
HelloRanges/man/bedtools_intersect.Rd
HelloRanges/man/bedtools_jaccard.Rd
HelloRanges/man/bedtools_makewindows.Rd
HelloRanges/man/bedtools_map.Rd
HelloRanges/man/bedtools_merge.Rd
HelloRanges/man/bedtools_multiinter.Rd
HelloRanges/man/bedtools_nuc.Rd
HelloRanges/man/bedtools_shift.Rd
HelloRanges/man/bedtools_slop.Rd
HelloRanges/man/bedtools_subtract.Rd
HelloRanges/man/bedtools_unionbedg.Rd
HelloRanges/man/distmode.Rd
HelloRanges/man/pair.Rd
HelloRanges/tests
HelloRanges/tests/HelloRanges_unit_tests.R
HelloRanges/vignettes
HelloRanges/vignettes/auto
HelloRanges/vignettes/auto/tutorial.el
HelloRanges/vignettes/fig
HelloRanges/vignettes/fig/complement.jpg
HelloRanges/vignettes/fig/genomecov.jpg
HelloRanges/vignettes/fig/intersect.jpg
HelloRanges/vignettes/fig/merge.jpg
HelloRanges/vignettes/tutorial.Rnw
HelloRanges/vignettes/tutorial.bib