HelloRanges: Introduce *Ranges to bedtools users
Version 1.2.0

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
Bioconductor views Annotation Coverage DataImport GenomeAnnotation SequenceMatching Sequencing VariantAnnotation
Date of publicationNone
MaintainerMichael Lawrence <michafla@gene.com>
LicenseGPL (>= 2)
Version1.2.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("HelloRanges")

Popular man pages

argparse: Argument parsing details
bedtools_closest: bedtools_closest
bedtools_coverage: bedtools_coverage
bedtools_genomecov: bedtools_genomecov
bedtools_intersect: bedtools_intersect
bedtools_multiinter: bedtools_multiinter
bedtools_shift: bedtools_shift
See all...

All man pages Function index File listing

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

Functions

GenomeFile Source code
NAGRanges Source code
R Source code Source code
R_bedtools_closest Man page Source code
R_bedtools_complement Man page Source code
R_bedtools_coverage Man page Source code
R_bedtools_disjoin Source code
R_bedtools_flank Man page Source code
R_bedtools_genomecov Man page Source code
R_bedtools_getfasta Man page Source code
R_bedtools_groupby Man page Source code
R_bedtools_intersect Man page Source code
R_bedtools_jaccard Man page Source code
R_bedtools_makewindows Man page Source code
R_bedtools_map Man page Source code
R_bedtools_merge Man page Source code
R_bedtools_multiinter Man page Source code
R_bedtools_nuc Man page Source code
R_bedtools_shift Man page Source code
R_bedtools_slop Man page Source code
R_bedtools_subtract Man page Source code
R_bedtools_unionbedg Man page Source code
aggregateCall Source code
argparsing Man page
bedtools_closest Man page Source code
bedtools_complement Man page Source code
bedtools_coverage Man page Source code
bedtools_flank Man page Source code
bedtools_genomecov Man page Source code
bedtools_getfasta Man page Source code
bedtools_groupby Man page Source code
bedtools_intersect Man page Source code
bedtools_jaccard Man page Source code
bedtools_makewindows Man page Source code
bedtools_map Man page Source code
bedtools_merge Man page Source code
bedtools_multiinter Man page Source code
bedtools_nuc Man page Source code
bedtools_shift Man page Source code
bedtools_slop Man page Source code
bedtools_subtract Man page Source code
bedtools_unionbedg Man page Source code
coerceOpts Source code
distmode Man page
distmode,CompressedAtomicList-method Man page
distmode,SimpleList-method Man page
distmode,factor-method Man page
distmode,vector-method Man page
do_R_call Source code
do_bedtools_closest Man page
do_bedtools_complement Man page
do_bedtools_coverage Man page
do_bedtools_flank Man page
do_bedtools_genomecov Man page
do_bedtools_getfasta Man page
do_bedtools_groupby Man page
do_bedtools_intersect Man page
do_bedtools_jaccard Man page
do_bedtools_makewindows Man page
do_bedtools_map Man page
do_bedtools_merge Man page
do_bedtools_multiinter Man page
do_bedtools_nuc Man page
do_bedtools_shift Man page
do_bedtools_slop Man page
do_bedtools_subtract Man page
do_bedtools_unionbedg Man page
findOverlaps Source code
getFormat Source code
getR Source code
hasFormat Source code
hasRanges Source code
importA Source code
importB Source code
importExtraColsArgs Source code
importGenome Source code
intersectPairs Source code
isBam Source code
isBed Source code
isResource Source code
isVcf Source code
makeNAColumn Source code
make_do Source code
normA Source code
normB Source code
normCandO Source code
normG Source code
objectName Source code
overlapWidth Source code
pair Man page
pair,GAlignments,GenomicRanges-method Man page
pair,GenomicRanges,GenomicRanges-method Man page
pair,SummarizedExperiment,GenomicRanges-method Man page
pair,Vector,Vector-method Man page
pipeFile Source code
prepAnsRanges Source code
prepOverlapRanges Source code
preprocessCmd Source code
pushR Source code
restrictByFraction Source code
stdinFile Source code
substituteArgs Source code
test Source code
toparent Source code

Files

DESCRIPTION
NAMESPACE
R
R/a.R
R/closest.R
R/complement.R
R/coverage.R
R/flank.R
R/genomecov.R
R/getfasta.R
R/groupby.R
R/intersect.R
R/jaccard.R
R/makewindows.R
R/map.R
R/merge.R
R/multiinter.R
R/nuc.R
R/shift.R
R/slop.R
R/subtract.R
R/test_HelloRanges_package.R
R/unionbedg.R
R/utils.R
build
build/vignette.rds
inst
inst/NEWS
inst/doc
inst/doc/tutorial.R
inst/doc/tutorial.Rnw
inst/doc/tutorial.pdf
inst/unitTests
inst/unitTests/data
inst/unitTests/data/closest
inst/unitTests/data/closest/a.bed
inst/unitTests/data/closest/b.bed
inst/unitTests/data/closest/close-a.bed
inst/unitTests/data/closest/close-b.bed
inst/unitTests/data/closest/d.bed
inst/unitTests/data/closest/d_id.bed
inst/unitTests/data/closest/d_iu.bed
inst/unitTests/data/closest/mdb1.bed
inst/unitTests/data/closest/mdb2.bed
inst/unitTests/data/closest/mdb3.bed
inst/unitTests/data/closest/mq1.bed
inst/unitTests/data/closest/strand-test-a.bed
inst/unitTests/data/closest/strand-test-b.bed
inst/unitTests/data/coverage
inst/unitTests/data/coverage/a.bed
inst/unitTests/data/coverage/b.bed
inst/unitTests/data/coverage/test.genome
inst/unitTests/data/flank
inst/unitTests/data/flank/a.bed
inst/unitTests/data/flank/tiny.genome
inst/unitTests/data/genomecov
inst/unitTests/data/genomecov/chip.sam
inst/unitTests/data/genomecov/pair-chip.sam
inst/unitTests/data/genomecov/sam-w-del.sam
inst/unitTests/data/genomecov/test.genome
inst/unitTests/data/genomecov/three_blocks.sam
inst/unitTests/data/genomecov/y.bam
inst/unitTests/data/genomecov/y.bed
inst/unitTests/data/getfasta
inst/unitTests/data/getfasta/blocks.bed
inst/unitTests/data/getfasta/t.fa
inst/unitTests/data/groupby
inst/unitTests/data/groupby/a_vcfSVtest.vcf
inst/unitTests/data/groupby/values3.header.bed
inst/unitTests/data/intersect
inst/unitTests/data/intersect/a.bed
inst/unitTests/data/intersect/b.bed
inst/unitTests/data/intersect/c.bed
inst/unitTests/data/intersect/d.bed
inst/unitTests/data/intersect/one_block.sam
inst/unitTests/data/intersect/three_blocks.sam
inst/unitTests/data/intersect/three_blocks_match.bed
inst/unitTests/data/intersect/three_blocks_match_1bp.bed
inst/unitTests/data/intersect/three_blocks_nomatch.bed
inst/unitTests/data/intersect/two_blocks.sam
inst/unitTests/data/intersect/x.bed
inst/unitTests/data/intersect/y.bed
inst/unitTests/data/jaccard
inst/unitTests/data/jaccard/a.bam
inst/unitTests/data/jaccard/a.bed
inst/unitTests/data/jaccard/aMixedStrands.bed
inst/unitTests/data/jaccard/bMixedStrands.bed
inst/unitTests/data/jaccard/e.bed
inst/unitTests/data/jaccard/three_blocks_match.bam
inst/unitTests/data/jaccard/three_blocks_match.bed
inst/unitTests/data/makewindows
inst/unitTests/data/makewindows/input.bed
inst/unitTests/data/makewindows/test.genome
inst/unitTests/data/map
inst/unitTests/data/map/ivls.bed
inst/unitTests/data/map/ivls2.bed
inst/unitTests/data/map/test.gff2
inst/unitTests/data/map/values.bed
inst/unitTests/data/map/values5.bed
inst/unitTests/data/merge
inst/unitTests/data/merge/a.bed
inst/unitTests/data/merge/a.full.bed
inst/unitTests/data/merge/a.names.bed
inst/unitTests/data/merge/fullFields.bam
inst/unitTests/data/merge/testA.vcf
inst/unitTests/data/multiinter
inst/unitTests/data/multiinter/a.bed
inst/unitTests/data/multiinter/b.bed
inst/unitTests/data/multiinter/c.bed
inst/unitTests/data/multiinter/test.genome
inst/unitTests/data/nuc
inst/unitTests/data/nuc/a.bed
inst/unitTests/data/nuc/test.fasta
inst/unitTests/data/shift
inst/unitTests/data/shift/a.bed
inst/unitTests/data/shift/tiny.genome
inst/unitTests/data/slop
inst/unitTests/data/slop/a.bed
inst/unitTests/data/slop/tiny.genome
inst/unitTests/data/subtract
inst/unitTests/data/subtract/a.bed
inst/unitTests/data/subtract/b.bed
inst/unitTests/data/subtract/c.bed
inst/unitTests/data/subtract/d.bed
inst/unitTests/data/unionbedg
inst/unitTests/data/unionbedg/a.bedGraph
inst/unitTests/data/unionbedg/b.bedGraph
inst/unitTests/data/unionbedg/c.bedGraph
inst/unitTests/data/unionbedg/test.genome
inst/unitTests/test_closest.R
inst/unitTests/test_coverage.R
inst/unitTests/test_flank.R
inst/unitTests/test_genomecov.R
inst/unitTests/test_getfasta.R
inst/unitTests/test_groupby.R
inst/unitTests/test_intersect.R
inst/unitTests/test_jaccard.R
inst/unitTests/test_makewindows.R
inst/unitTests/test_map.R
inst/unitTests/test_merge.R
inst/unitTests/test_multiinter.R
inst/unitTests/test_nuc.R
inst/unitTests/test_shift.R
inst/unitTests/test_slop.R
inst/unitTests/test_subtract.R
inst/unitTests/test_unionbedg.R
man
man/argparse.Rd
man/bedtools_closest.Rd
man/bedtools_complement.Rd
man/bedtools_coverage.Rd
man/bedtools_flank.Rd
man/bedtools_genomecov.Rd
man/bedtools_getfasta.Rd
man/bedtools_groupby.Rd
man/bedtools_intersect.Rd
man/bedtools_jaccard.Rd
man/bedtools_makewindows.Rd
man/bedtools_map.Rd
man/bedtools_merge.Rd
man/bedtools_multiinter.Rd
man/bedtools_nuc.Rd
man/bedtools_shift.Rd
man/bedtools_slop.Rd
man/bedtools_subtract.Rd
man/bedtools_unionbedg.Rd
man/distmode.Rd
man/pair.Rd
tests
tests/HelloRanges_unit_tests.R
vignettes
vignettes/auto
vignettes/auto/tutorial.el
vignettes/fig
vignettes/fig/complement.jpg
vignettes/fig/genomecov.jpg
vignettes/fig/intersect.jpg
vignettes/fig/merge.jpg
vignettes/tutorial.Rnw
vignettes/tutorial.bib
HelloRanges documentation built on May 20, 2017, 9:54 p.m.

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