Package: bedr 1.0.7

bedr: Genomic Region Processing using Tools Such as 'BEDTools', 'BEDOPS' and 'Tabix'

Genomic regions processing using open-source command line tools such as 'BEDTools', 'BEDOPS' and 'Tabix'. These tools offer scalable and efficient utilities to perform genome arithmetic e.g indexing, formatting and merging. bedr API enhances access to these tools as well as offers additional utilities for genomic regions processing.

Authors:Syed Haider [aut], Daryl Waggott [aut], Emilie Lalonde [ctb], Clement Fung [ctb], Paul C. Boutros [aut, cre, cph]

bedr_1.0.7.tar.gz
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bedr.pdf |bedr.html✨
bedr/json (API)
NEWS

# Install 'bedr' in R:
install.packages('bedr', repos = c('https://pboutros.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

On CRAN:

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

4.19 score 2 packages 257 scripts 780 downloads 42 exports 41 dependencies

Last updated 6 years agofrom:579f884498. Checks:OK: 5 NOTE: 2. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 29 2024
R-4.5-winNOTEOct 29 2024
R-4.5-linuxNOTEOct 29 2024
R-4.4-winOKOct 29 2024
R-4.4-macOKOct 29 2024
R-4.3-winOKOct 29 2024
R-4.3-macOKOct 29 2024

Exports:%in.region%bed2indexbed2vcfbedrbedr.join.multiple.regionbedr.join.regionbedr.merge.regionbedr.plot.regionbedr.setupbedr.snm.regionbedr.sort.regionbedr.subtract.regioncatvcheck.binarycluster.regionconvert2beddownload.datasetsflank.regionget.chr.lengthget.example.regionsget.fastaget.random.regionsgrow.regionin.regionindex2bedis.merged.regionis.sorted.regionis.valid.refis.valid.regionis.valid.seqjaccardorder.regionpermute.regionprocess.inputquery.ucscread.vcfreldiststrsplit2matrixtabixtest.region.similarityvcf2bedwrite.vcf

Dependencies:briocallrclicrayondata.tabledescdiffobjdigestevaluatefansiformatRfsfutile.loggerfutile.optionsgluejsonlitelambda.rlifecyclemagrittrpillarpkgbuildpkgconfigpkgloadpraiseprocessxpsR.methodsS3R.ooR.utilsR6rematch2rlangrprojroottestthattibbleutf8vctrsVennDiagramwaldowithryaml

Rendered fromUsing-bedr.Rmdusingknitr::rmarkdownon Oct 29 2024.

Last update: 2019-04-01
Started: 2015-09-04

Readme and manuals

Help Manual

Help pageTopics
A bedtools wrapper for working with genomic ranges in Rbedr-package
checks if regions in object a are found in object b%in.region%
bed dataframe to index stringbed2index
convert bed to vcfbed2vcf
Main bedtools wrapper function.bedr
join multiple region objectsbedr.join.multiple.region
join two region objects using a left outer joinbedr.join.region
merge i.e. collapse overlpaping regionsbedr.merge.region
Visualize regions or intervalsbedr.plot.region
Initialize some config settings for bedrbedr.setup
sort a region filebedr.snm.region
sort a region filebedr.sort.region
subtracts features or ranges in object b from object abedr.subtract.region
outputs text if verbose flag is setcatv
checks if binary is in the pathcheck.binary
cluster intervalscluster.region
convert object to bed formatconvert2bed
output R objects as tmpfilescreate.tmp.bed.file
Determine input formatdetermine.input
Data frame to list conversiondf2list
Download some useful datasetsdownload.datasets
Get adjacent flanks from regionsflank.region
gets the length of each chromosome for a species/buildget.chr.length
return a set of regions for the examples and unit testingget.example.regions
Query fasta sequenceget.fasta
generates a set of random regionsget.random.regions
Get adjacent flanks from regionsgrow.region
checks if regions in object a are found in object bin.region
convert a region index into a bed file dataframeindex2bed
checks if region file is mergedis.merged.region
checks if region file is sortedis.sorted.region
verifies the reference sequence in a vcfis.valid.ref
checks if region/index is validis.valid.region
verifies that sequences are correct given coordinates and a referenceis.valid.seq
calculate the jaccard distance between sets of intervalsjaccard
Interface to R's modifyListmodifyList2
Gets the sort order of a region index similar to the order commandorder.region
permute a set of regionspermute.region
process.inputprocess.input
read a ucsc table into Rquery.ucsc
Read a vcf into Rread.vcf
Calculate the relative distance between two sets of intervalsreldist
Get region sizesize.region
split a vector of strings into tabular datastrsplit2matrix
Main bedtools wrapper function.tabix
Plot venn diagramtable2venn
Compare sets of regions via jaccard and relative distance using permutationtest.region.similarity
convert a vcf to a bed filevcf2bed
write a vcf objectwrite.vcf