├── .Rbuildignore ├── .github ├── .gitignore └── workflows │ └── R-CMD-check.yaml ├── .gitignore ├── DESCRIPTION ├── LICENSE ├── LICENSE.md ├── NAMESPACE ├── R ├── bt.annotate.R ├── bt.bamtobed.R ├── bt.bamtofastq.R ├── bt.bed12tobed6.R ├── bt.bedpetobam.R ├── bt.bedtobam.R ├── bt.closest.R ├── bt.cluster.R ├── bt.complement.R ├── bt.coverage.R ├── bt.expand.R ├── bt.fisher.R ├── bt.flank.R ├── bt.genomecov.R ├── bt.getfasta.R ├── bt.groupby.R ├── bt.igv.R ├── bt.intersect.R ├── bt.jaccard.R ├── bt.links.R ├── bt.makewindows.R ├── bt.map.R ├── bt.maskfasta.R ├── bt.merge.R ├── bt.multicov.R ├── bt.multiinter.R ├── bt.nuc.R ├── bt.overlap.R ├── bt.pairtobed.R ├── bt.pairtopair.R ├── bt.random.R ├── bt.reldist.R ├── bt.sample.R ├── bt.shift.R ├── bt.shuffle.R ├── bt.slop.R ├── bt.sort.R ├── bt.spacing.R ├── bt.split.R ├── bt.subtract.R ├── bt.summary.R ├── bt.tag.R ├── bt.unionbedg.R ├── bt.window.R ├── createOptions.R ├── deleteTempFiles.R ├── establishPaths.R └── zzz.R ├── README.md ├── bedtoolsr.Rproj ├── dev ├── anomalies.json ├── createOptions.R ├── deleteTempFiles.R ├── document.R ├── establishPaths.R ├── makePackage.py └── zzz.R ├── extdata ├── dm6 ├── hg19 ├── hg38 ├── mm10 └── mm9 ├── img └── exampleResults.png ├── inst ├── extdata │ ├── dm6 │ ├── hg19 │ ├── hg38 │ ├── mm10 │ └── mm9 └── tests │ ├── testthat.R │ └── testthat │ ├── test-bt.annotate.R │ ├── test-bt.closest.R │ ├── test-bt.cluster.R │ ├── test-bt.complement.R │ ├── test-bt.coverage.R │ ├── test-bt.expand.R │ ├── test-bt.fisher.R │ ├── test-bt.flank.R │ ├── test-bt.genomecov.R │ ├── test-bt.groupby.R │ ├── test-bt.intersect.R │ ├── test-bt.jaccard.R │ ├── test-bt.makewindows.R │ ├── test-bt.map.R │ ├── test-bt.merge.R │ ├── test-bt.overlap.R │ ├── test-bt.shift.R │ ├── test-bt.shuffle.R │ ├── test-bt.slop.R │ ├── test-bt.sort.R │ ├── test-bt.spacing.R │ ├── test-bt.subtract.R │ ├── test-bt.unionbedg.R │ └── test-bt.window.R ├── man ├── bt.annotate.Rd ├── bt.bamtobed.Rd ├── bt.bamtofastq.Rd ├── bt.bed12tobed6.Rd ├── bt.bedpetobam.Rd ├── bt.bedtobam.Rd ├── bt.closest.Rd ├── bt.cluster.Rd ├── bt.complement.Rd ├── bt.coverage.Rd ├── bt.expand.Rd ├── bt.fisher.Rd ├── bt.flank.Rd ├── bt.genomecov.Rd ├── bt.getfasta.Rd ├── bt.groupby.Rd ├── bt.igv.Rd ├── bt.intersect.Rd ├── bt.jaccard.Rd ├── bt.links.Rd ├── bt.makewindows.Rd ├── bt.map.Rd ├── bt.maskfasta.Rd ├── bt.merge.Rd ├── bt.multicov.Rd ├── bt.multiinter.Rd ├── bt.nuc.Rd ├── bt.overlap.Rd ├── bt.pairtobed.Rd ├── bt.pairtopair.Rd ├── bt.random.Rd ├── bt.reldist.Rd ├── bt.sample.Rd ├── bt.shift.Rd ├── bt.shuffle.Rd ├── bt.slop.Rd ├── bt.sort.Rd ├── bt.spacing.Rd ├── bt.split.Rd ├── bt.subtract.Rd ├── bt.summary.Rd ├── bt.tag.Rd ├── bt.unionbedg.Rd ├── bt.window.Rd ├── createOptions.Rd ├── deleteTempFiles.Rd └── establishPaths.Rd ├── paper ├── paper.bib └── paper.md └── tests ├── testthat.R └── testthat ├── test-bt.annotate.R ├── test-bt.closest.R ├── test-bt.cluster.R ├── test-bt.complement.R ├── test-bt.coverage.R ├── 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