Files in bedr
Genomic Region Processing using Tools Such as 'BEDTools', 'BEDOPS' and 'Tabix'
MD5
NEWS.md
NAMESPACE
DESCRIPTION
R/bedr.sort.region.R
R/jaccard.R
R/strsplit2matrix.R
R/index2bed.R
R/is.valid.ref.R
R/is.valid.seq.R
R/size.region.R
R/bedr.plot.region.R
R/get.example.regions.R
R/flank.region.R
R/cluster.region.R
R/download.datasets.R
R/bed2index.R
R/convert2bed.R
R/bedr.merge.region.R
R/read.vcf.R
R/is.valid.region.R
R/get.strand.R
R/bedr.setup.R
R/modifyList2.R
R/bedr.snm.region.R
R/permute.region.R
R/bed2vcf.R
R/in.region.R
R/onAttach.R
R/check.binary.R
R/bedr.R
R/vcf2bed.R
R/is.merged.region.R
R/df2list.R
R/query.ucsc.R
R/vcf2bedpe.R
R/get.random.regions.R
R/reldist.R
R/test.region.similarity.R
R/is.sorted.region.R
R/create.tmp.bed.file.R
R/order.region.R
R/bedr.subtract.region.R
R/bedr.join.region.R
R/tabix.R
R/determine.input.R
R/table2venn.R
R/get.fasta.R
R/grow.region.R
R/catv.R
R/adjust.coordinates.R
R/get.bedpe.id.R
R/get.chr.length.R
R/write.vcf.R
R/process.input.R
R/bedr.join.multiple.region.R
inst/doc/Using-bedr.Rmd
inst/doc/Using-bedr.html
inst/doc/Using-bedr.R
inst/extdata/example-a-region.bed
inst/extdata/callerB.vcf.gz
inst/extdata/clinvar_dbSNP138_example.vcf.gz
inst/extdata/CosmicCodingMuts_v66_20130725_ex.vcf.gz.tbi
inst/extdata/callerA.vcf.gz
inst/extdata/ucsc.hg19.example.fasta
inst/extdata/singleSampleOICR_example.vcf.gz
inst/extdata/multiSampleOICR_example.vcf.gz
inst/extdata/ucsc.hg19.RefSeq.chr1-2.txt.gz
inst/extdata/ucsc.hg19.example.fasta.fai
inst/extdata/CNA.segmented.txt.gz
inst/extdata/ucsc.hg19.chrM.fasta
inst/extdata/CosmicCodingMuts_v66_20130725_ex.vcf.gz
inst/extdata/ucsc.hg19.chrM.fasta.fai
inst/extdata/gridssSV.vcf.gz
inst/config/config.yaml
inst/genomes/mouse.mm8.genome
inst/genomes/human.hg18.genome
inst/genomes/human.hg38.genome
inst/genomes/human.hg19.genome
inst/genomes/mouse.mm9.genome
build/vignette.rds
tests/testthat.R
tests/testthat/test-process.input.R
tests/testthat/test-convert2bed.R
tests/testthat/test-vcf2bedpe.R
tests/testthat/test-in.region.R
tests/testthat/test-tabix.R
tests/testthat/test-determine.input.R
tests/testthat/test-is.sorted.region.R
tests/testthat/test-is.merged.region.R
tests/testthat/test-sort.region.R
tests/testthat/test-index2bed.R
tests/testthat/test-is.valid.region.R
tests/testthat/data/example-a-region.bed
tests/testthat/data/mantaSV.vcf.gz
tests/testthat/data/callerB.vcf.gz
tests/testthat/data/dellySV.vcf.gz
tests/testthat/data/clinvar_dbSNP138_example.vcf.gz
tests/testthat/data/CosmicCodingMuts_v66_20130725_ex.vcf.gz.tbi
tests/testthat/data/callerA.vcf.gz
tests/testthat/data/ucsc.hg19.example.fasta
tests/testthat/data/gap.txt.gz
tests/testthat/data/singleSampleOICR_example.vcf.gz
tests/testthat/data/multiSampleOICR_example.vcf.gz
tests/testthat/data/gap.sql
tests/testthat/data/ucsc.hg19.RefSeq.chr1-2.txt.gz
tests/testthat/data/rmsk.sql
tests/testthat/data/ucsc.hg19.example.fasta.fai
tests/testthat/data/CNA.segmented.txt.gz
tests/testthat/data/ucsc.hg19.chrM.fasta
tests/testthat/data/CosmicCodingMuts_v66_20130725_ex.vcf.gz
tests/testthat/data/ucsc.hg19.chrM.fasta.fai
tests/testthat/data/gridssSV.vcf.gz
vignettes/Using-bedr.Rmd
vignettes/GitHub2.css
man/bed2index.Rd
man/order.region.Rd
man/convert2bed.Rd
man/get.strand.Rd
man/download.datasets.Rd
man/query.ucsc.Rd
man/bed2vcf.Rd
man/get.example.regions.Rd
man/strsplit2matrix.Rd
man/bedr.subtract.region.Rd
man/create.tmp.bed.file.Rd
man/df2list.Rd
man/bedr.join.multiple.region.Rd
man/get.chr.length.Rd
man/index2bed.Rd
man/get.bedpe.id.Rd
man/process.input.Rd
man/grow.region.Rd
man/bedr.Rd
man/read.vcf.Rd
man/is.sorted.region.Rd
man/flank.region.Rd
man/bedr.merge.region.Rd
man/is.valid.ref.Rd
man/jaccard.Rd
man/is.valid.region.Rd
man/bedr.sort.region.Rd
man/get.random.regions.Rd
man/in.region2.Rd
man/write.vcf.Rd
man/in.region.Rd
man/tabix.Rd
man/bedr.plot.region.Rd
man/check.binary.Rd
man/is.merged.region.Rd
man/test.region.similarity.Rd
man/permute.region.Rd
man/adjust.coordinates.Rd
man/table2venn.Rd
man/vcf2bed.Rd
man/size.region.Rd
man/bedr.snm.region.Rd
man/get.fasta.Rd
man/bedr.join.region.Rd
man/bedr.setup.Rd
man/determine.input.Rd
man/is.valid.seq.Rd
man/cluster.region.Rd
man/reldist.Rd
man/vcf2bedpe.Rd
man/modifyList2.Rd
man/catv.Rd
