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bedr  

Genomic Region Processing using Tools Such as 'BEDTools', 'BEDOPS' and 'Tabix'
View on CRAN: Click here


Download and install bedr package within the R console
Install from CRAN:
install.packages("bedr")

Install from Github:
library("remotes")
install_github("cran/bedr")

Install by package version:
library("remotes")
install_version("bedr", "1.1.3")



Attach the package and use:
library("bedr")
Maintained by
Paul C. Boutros
[Scholar Profile | Author Map]
First Published: 2015-09-04
Latest Update: 2019-04-01
Description:
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.
How to cite:
Paul C. Boutros (2015). bedr: Genomic Region Processing using Tools Such as 'BEDTools', 'BEDOPS' and 'Tabix'. R package version 1.1.3, https://cran.r-project.org/web/packages/bedr. Accessed 01 May. 2025.
Previous versions and publish date:
1.0.0 (2015-09-04 21:49), 1.0.1 (2015-09-05 17:51), 1.0.2 (2015-09-21 17:58), 1.0.3 (2016-08-23 18:04), 1.0.4 (2017-10-13 23:27), 1.0.6 (2019-01-13 00:32), 1.0.7 (2019-04-01 20:50)
Other packages that cited bedr R package
View bedr citation profile
Other R packages that bedr depends, imports, suggests or enhances
Complete documentation for bedr
Functions, R codes and Examples using the bedr R package
Some associated functions: bed2index . bed2vcf . bedR-package . bedr.join.multiple.region . bedr.join.region . bedr.merge.region . bedr . bedr.plot.region . bedr.setup . bedr.snm.region . bedr.sort.region . bedr.subtract.region . catv . check.binary . cluster.region . convert2bed . create.tmp.bed.file . determine.input . df2list . download.datasets . flank.region . get.chr.length . get.example.regions . get.fasta . get.random.regions . grow.region . in.region . in.region2 . index2bed . is.merged.region . is.sorted.region . is.valid.ref . is.valid.region . is.valid.seq . jaccard . modifyList2 . order.region . permute.region . process.input . query.ucsc . read.vcf . reldist . size.region . strsplit2matrix . tabix . table2venn . test.region.similarity . vcf2bed . write.vcf . 
Some associated R codes: bed2index.R . bed2vcf.R . bedr.R . bedr.join.multiple.region.R . bedr.join.region.R . bedr.merge.region.R . bedr.plot.region.R . bedr.setup.R . bedr.snm.region.R . bedr.sort.region.R . bedr.subtract.region.R . catv.R . check.binary.R . cluster.region.R . convert2bed.R . create.tmp.bed.file.R . determine.input.R . df2list.R . download.datasets.R . flank.region.R . get.chr.length.R . get.example.regions.R . get.fasta.R . get.random.regions.R . grow.region.R . in.region.R . index2bed.R . is.merged.region.R . is.sorted.region.R . is.valid.ref.R . is.valid.region.R . is.valid.seq.R . jaccard.R . modifyList2.R . onAttach.R . order.region.R . permute.region.R . process.input.R . query.ucsc.R . read.vcf.R . reldist.R . size.region.R . strsplit2matrix.R . tabix.R . table2venn.R . test.region.similarity.R . vcf2bed.R . write.vcf.R .  Full bedr package functions and examples
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