├── .DS_Store ├── .Rbuildignore ├── .gitignore ├── DESCRIPTION ├── LICENSE ├── LICENSE.md ├── NAMESPACE ├── NEWS.md ├── R ├── assign_neighbourhoods.R ├── calc_AUC_per_neighbourhood.R ├── convert_de_stat.R ├── de_test_neighbourhoods.R ├── estimate_neighbourhood_sizes.R ├── filter_neighbourhoods.R ├── plotting_functions.R ├── rank_neighbourhoods_by_DE_magnitude.R ├── sce_mouseEmbryo.R ├── spatial_pval_adjustment.R └── utils.R ├── README.md ├── data-raw └── sce_mouseEmbryo.R ├── data └── sce_mouseEmbryo.rda ├── man ├── assign_neighbourhoods.Rd ├── calc_AUC_per_neighbourhood.Rd ├── convert_de_stat.Rd ├── de_test_neighbourhoods.Rd ├── de_test_single_neighbourhood.Rd ├── estimate_neighbourhood_sizes.Rd ├── filter_neighbourhoods.Rd ├── plot_DE_gene_set.Rd ├── plot_DE_single_gene.Rd ├── plot_beeswarm_gene_set.Rd ├── plot_beeswarm_single_gene.Rd ├── plot_milo_by_single_metric.Rd ├── rank_neighbourhoods_by_DE_magnitude.Rd ├── sce_mouseEmbryo.Rd └── spatial_pval_adjustment.Rd ├── miloDE.Rproj ├── miloDE_cartoon.png ├── tests ├── .DS_Store ├── testthat.R └── testthat │ ├── test-all_arguments_for_buildGraph.R │ ├── test-assign_neighbourhoods.R │ ├── test-calc_AUC_per_neighbourhood.R │ ├── test-convert_de_stat.R │ ├── test-de_test_neighbourhoods.R │ ├── test-estimate_neighbourhood_sizes.R │ ├── test-filter_neighbourhoods.R │ ├── test-rank_neighbourhoods_by_DE_magnitude.R │ └── test-spatial_pval_adjustment.R └── vignettes ├── .gitignore └── miloDE__mouse_embryo.Rmd /.DS_Store: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MarioniLab/miloDE/HEAD/.DS_Store -------------------------------------------------------------------------------- /.Rbuildignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MarioniLab/miloDE/HEAD/.Rbuildignore -------------------------------------------------------------------------------- /.gitignore: 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