├── .gitignore ├── .gitmodules ├── LICENSE ├── README.md ├── benchmark ├── Fig2_benchmark_results.Rmd ├── Fig2_benchmark_results.nb.html ├── README.md ├── benchmark_DAsize │ ├── run_DA_size_capped.r │ └── submit_benchmark_capped.sh ├── benchmark_Kselection │ └── submit_k_selection.sh ├── benchmark_MNN │ └── submit_benchmark_MNN.sh ├── benchmark_main │ ├── build_outcome.R │ └── submit_benchmark.sh ├── benchmark_make_data │ ├── make_bm_data.R │ ├── make_bm_data_clusters.R │ └── submit_make_bm_data.sh ├── benchmark_miloVSmeld │ ├── run_meld.py │ ├── run_miloVSmeld.R │ └── submit_meldVSmilo.sh ├── benchmark_utils.R └── run_DA_R.r ├── ms ├── figures │ ├── milo_figures.Rmd │ ├── milo_figures.out │ ├── milo_figures.pdf │ └── milo_figures.tex └── supplement │ ├── cell-numeric.csl │ ├── milo_suppl_figures.Rmd │ ├── milo_suppl_figures.pdf │ ├── milo_suppl_figures.tex │ ├── milo_supplement.Rmd │ ├── milo_supplement.bib │ ├── milo_supplement.pdf │ ├── milo_supplement.tex │ ├── preamble.tex │ └── suppl_tables │ ├── suppl_tab1.csv │ ├── table_methods_comparison.pdf │ ├── table_methods_params.pdf │ └── table_simulation_params.pdf ├── notebooks ├── 2020-07-29_milo_graph_simulations.Rmd ├── 2020-08-13_k_nhSize_and_FDR.Rmd ├── 2020-09-14_methods_comparison.Rmd ├── 2020-09-24_Milo_scalability.Rmd ├── 2021-02-23_thymus_droplet_processing.Rmd ├── 2021-02-26_Milo_scalability.Rmd ├── Fig5_liver_cirrhosis.Rmd ├── Fig5_liver_cirrhosis.nb.html ├── SFig1_randomVSrefined_sampling.Rmd ├── SFig2_batch_effect_simulation.Rmd ├── SFig3_batch_effect_gastrulation.Rmd ├── milo_in_python.ipynb ├── mouse_DAcompare.Rmd ├── mouse_thymus-figures_revision.Rmd └── mousethymus_validation.Rmd └── simulations ├── discrete_simulations.R ├── generate_branching_trajectory.R └── trajectory_simulation.R /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MarioniLab/milo_analysis_2020/HEAD/.gitignore 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