├── .Rbuildignore ├── .github ├── .gitignore └── workflows │ ├── rworkflows.yml │ └── test-coverage.yaml ├── .gitignore ├── CODE_OF_CONDUCT.md ├── DESCRIPTION ├── LICENSE ├── NAMESPACE ├── NEWS.md ├── R ├── bamutils.R ├── data.R ├── footprint.R ├── fragsize.R ├── globals.R ├── nucleosome_enrichment.R ├── utils.R ├── vmat.R ├── vmat_utils.R └── vplot-chroms.R ├── README.md ├── codecov.yml ├── data ├── ABF1_sacCer3.rda ├── ATAC_ce11_Serizay2020.rda ├── CTCF_hg38.rda ├── MNase_sacCer3_Henikoff2011.rda ├── MNase_sacCer3_Henikoff2011_subset.rda ├── REB1_sacCer3.rda ├── bam_test.rda ├── ce11_all_REs.rda └── ce11_proms.rda ├── inst └── figures │ ├── concept.png │ ├── fragment_size_distribution.png │ ├── logo.png │ └── vplot.png ├── man ├── ABF1_sacCer3.Rd ├── ATAC_ce11_Serizay2020.Rd ├── CTCF_hg38.Rd ├── MNase_sacCer3_Henikoff2011.Rd ├── MNase_sacCer3_Henikoff2011_subset.Rd ├── REB1_sacCer3.Rd ├── alignToTSS.Rd ├── bam_test.Rd ├── ce11_all_REs.Rd ├── ce11_proms.Rd ├── computeNucleosomeEnrichmentOverBackground.Rd ├── computeVmat.Rd ├── deconvolveBidirectionalPromoters.Rd ├── getCuts.Rd ├── getFragmentsDistribution.Rd ├── importPEBamFiles.Rd ├── normalizeVmat.Rd ├── nucleosomeEnrichment.GRanges.Rd ├── nucleosomeEnrichment.Rd ├── nucleosomeEnrichment.Vmat.Rd ├── plotFootprint.Rd ├── plotProfile.Rd ├── plotVmat.GRanges.Rd ├── plotVmat.Rd ├── plotVmat.Vmat.Rd ├── plotVmat.VmatList.Rd ├── plotVmat.default.Rd ├── plotVmat.list.Rd ├── sampleGRanges.GRanges.Rd ├── sampleGRanges.Rd ├── shiftATACGranges.Rd ├── shuffleVmat.Rd └── theme_ggplot2.Rd ├── paper ├── figures │ ├── figures_example.png │ ├── figures_footprint.png │ ├── figures_fragsize.png │ ├── figures_locus.png │ └── figures_vplot.png ├── paper.bib └── paper.md ├── pkgdown ├── _pkgdown.yml └── favicon │ ├── apple-touch-icon-120x120.png │ ├── apple-touch-icon-152x152.png │ ├── apple-touch-icon-180x180.png │ ├── apple-touch-icon-60x60.png │ ├── apple-touch-icon-76x76.png │ ├── apple-touch-icon.png │ ├── 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