├── .DS_Store ├── .Rbuildignore ├── .github ├── .gitignore └── workflows │ └── R-CMD-check.yaml ├── .gitignore ├── DESCRIPTION ├── LICENSE ├── LICENSE.md ├── NAMESPACE ├── R ├── blank.plot.R ├── check.colour.R ├── count.recombinations.per.base.R ├── count.recombinations.per.genome.R ├── data.R ├── draw.genome.annotations.R ├── load.gubbins.GFF.R ├── load.phylogenetic.tree.R ├── load.ref.genome.GFF.R ├── load.taxon.metadata.R └── phylo.rcandy.plot.R ├── RCandy.Rproj ├── RCandy_1.0.0.pdf ├── README.Rmd ├── README.md ├── cran-comments.md ├── data └── RCandy.rda ├── inst ├── .DS_Store ├── CITATION ├── extdata │ ├── .DS_Store │ ├── Hungary19A-6.gff │ ├── ST320.final_tree.tre │ ├── ST320.recombination_predictions.gff │ └── ST320.tsv └── vignette-supp │ ├── unnamed-chunk-10-1.png │ ├── unnamed-chunk-11-1.png │ ├── unnamed-chunk-12-1.png │ ├── unnamed-chunk-13-1.png │ ├── unnamed-chunk-14-1.png │ ├── unnamed-chunk-15-1.png │ ├── unnamed-chunk-16-1.png │ ├── unnamed-chunk-17-1.png │ ├── unnamed-chunk-18-1.png │ ├── unnamed-chunk-19-1.png │ ├── unnamed-chunk-20-1.png │ ├── unnamed-chunk-21-1.png │ ├── unnamed-chunk-22-1.png │ ├── unnamed-chunk-23-1.png │ ├── unnamed-chunk-24-1.png │ ├── unnamed-chunk-3-1.png │ ├── unnamed-chunk-4-1.png │ ├── unnamed-chunk-5-1.png │ ├── unnamed-chunk-6-1.png │ ├── unnamed-chunk-7-1.png │ ├── unnamed-chunk-8-1.png │ └── unnamed-chunk-9-1.png ├── man ├── .DS_Store ├── RCandyVis.Rd ├── count.rec.events.per.base.Rd ├── count.rec.events.per.genome.Rd ├── is.color.Rd ├── load.genome.GFF.Rd ├── load.gubbins.GFF.Rd ├── load.taxon.metadata.Rd ├── quote-RCandy-quote.Rd ├── read.tree.file.Rd ├── show.blank.plot.Rd └── show.genome.annotation.plot.Rd └── vignettes ├── .gitignore └── Introduction.Rmd /.DS_Store: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ChrispinChaguza/RCandy/HEAD/.DS_Store -------------------------------------------------------------------------------- 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