├── .Rbuildignore ├── .gitignore ├── .travis.yml ├── COPYING ├── DESCRIPTION ├── LICENSE ├── NAMESPACE ├── R ├── Drosophila_data.R ├── TOY24_data.R ├── blockUtility.R ├── checkInfile.R ├── computeRearrs.R ├── convertPQtree.R ├── filterRearrs.R ├── genome2PQtree.R ├── genomeImagePlot.R ├── genomeRearrPlot.R ├── getBreakpoints.R ├── orderGenomeMap.R ├── plotUtility.R ├── rearrUtility.R ├── rearrvisr.R ├── summarizeBlocks.R └── summarizeRearrs.R ├── README.Rmd ├── README.md ├── data ├── MEL_markers.rda ├── MSSYE_PQTREE_HEUR.rda ├── SIM_markers.rda ├── TOY24_compgenome.rda ├── TOY24_focalgenome.rda └── YAK_markers.rda ├── exec ├── convertPQtree.pl └── oma2anges.R ├── man ├── MEL_markers.Rd ├── MSSYE_PQTREE_HEUR.Rd ├── SIM_markers.Rd ├── TOY24_compgenome.Rd ├── TOY24_focalgenome.Rd ├── YAK_markers.Rd ├── checkInfile.Rd ├── computeRearrs.Rd ├── convertPQtree.Rd ├── filterRearrs.Rd ├── genome2PQtree.Rd ├── genomeImagePlot.Rd ├── genomeRearrPlot.Rd ├── getBreakpoints.Rd ├── orderGenomeMap.Rd ├── rearrvisr.Rd ├── summarizeBlocks.Rd └── summarizeRearrs.Rd ├── rearrvisr.Rproj ├── tests ├── testthat.R └── testthat │ ├── test.assignOri3.R │ ├── test.computeRearrs.R │ ├── test.makeBlocks.R │ └── test.tagTP2.R └── vignettes ├── Alignment.png ├── Classes.png ├── PQTree.png ├── Toy24_compgenome.png ├── bioinformatics.csl ├── rearrvisr.Rmd ├── rearrvisr.pdf └── rearrvisr_vignette.bib /.Rbuildignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dorolin/rearrvisr/HEAD/.Rbuildignore -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- 1 | ##inst/doc 2 | .Rproj.user 3 | -------------------------------------------------------------------------------- /.travis.yml: -------------------------------------------------------------------------------- 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