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.

AuthorMichael Lawrence
Date of publicationNone
MaintainerMichael Lawrence <michafla@gene.com>
LicenseGPL (>= 2)
Version1.0.1

View on Bioconductor

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

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