├── .Rbuildignore ├── .gitattributes ├── .github ├── .gitignore ├── CONTRIBUTING.md └── workflows │ ├── check-standard.yaml │ └── pkgdown.yaml ├── .gitignore ├── CODE_OF_CONDUCT.md ├── DESCRIPTION ├── LICENSE ├── NAMESPACE ├── NEWS.md ├── R ├── recomputeSupercells.R ├── runSuperCellCyto.R ├── simCytoData.R └── utils.R ├── README.md ├── _pkgdown.yml ├── inst ├── CITATION ├── README.md ├── extdata │ ├── Data23_Panel3_base_NR4_Patient9.fcs │ ├── Data23_Panel3_base_R5_Patient15.fcs │ ├── Levine_32dim_H1_sub.csv │ ├── Levine_32dim_H2_sub.csv │ ├── Levine_32dim_seurat_sub.qs2 │ └── Levine_32dim_subsampledPopulation.csv └── scripts │ └── make_levine_32dim.R ├── man ├── figures │ └── supercellcyto.png ├── recomputeSupercells.Rd ├── runSuperCellCyto.Rd └── simCytoData.Rd ├── tests ├── testthat.R └── testthat │ ├── test-recomputeSupercells.R │ ├── test-runSuperCellCyto.R │ ├── test-runSuperCellCyto_correctness.R │ ├── test-runSuperCellCyto_input.R │ └── test-simCytoData.R └── vignettes ├── 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