├── .Rbuildignore ├── .github ├── ISSUE_TEMPLATE │ ├── bug_report.md │ ├── feature_request.md │ └── question.md └── workflows │ └── run_tests.yml ├── .gitignore ├── DESCRIPTION ├── LICENSE ├── NAMESPACE ├── R ├── cluster.R ├── phate.R ├── preprocessing.R ├── tree.data.R └── utils.R ├── README.Rmd ├── README.md ├── data ├── tree.data.rda └── tree.data.small.rda ├── inst ├── CITATION ├── examples │ ├── bonemarrow_tutorial.Rmd │ └── bonemarrow_tutorial.html └── extdata │ └── generate_treedata.R ├── man ├── as.data.frame.Rd ├── as.matrix.Rd ├── check_pyphate_version.Rd ├── cluster_phate.Rd ├── figures │ ├── README-adjust-parameters-1.png │ ├── README-example-data-1.png │ ├── README-ggplot-1.png │ └── README-plot-results-1.png ├── ggplot.Rd ├── install.phate.Rd ├── library.size.normalize.Rd ├── phate.Rd ├── plot.Rd ├── print.Rd ├── summary.Rd ├── tree.data.Rd └── tree.data.small.Rd └── travis_setup.sh /.Rbuildignore: 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