├── .gitattributes ├── .github └── workflows │ ├── test_generate_dataset.yml │ ├── test_run_dataset_R.yml │ ├── test_run_dataset_cell2location.yml │ ├── test_run_dataset_dstg.yml │ ├── test_run_dataset_python.yml │ ├── test_run_dataset_spotlight.yml │ └── test_run_dataset_stereoscope.yml ├── .gitignore ├── Dockerfiles ├── Seurat 3.2.3 ├── Seurat 4.1.0 ├── Seurat 5.1.0 ├── SeuratDisk_0.0.0.9019 ├── SeuratDisk_0.0.0.9020 ├── SeuratDisk_Seurat3.2.3 ├── known_hosts └── synthspot ├── Guideline_for_adding_deconvolution_tools.md ├── LICENSE ├── README.md ├── bin ├── compute_metrics.R ├── run_music.R ├── run_rctd.R └── run_spotlight.R ├── conf ├── downsampling_liver.config ├── liver_exvivo.config ├── liver_mouse_visium.config ├── melanoma_visium.config ├── method_params_silver.yaml ├── ref_sensitivity_brain.config ├── ref_sensitivity_cerebellum.config ├── runtime.config ├── synthspot.yaml └── test.config ├── main.nf ├── nextflow.config ├── plots └── pr_curves_by_abundance │ ├── brain_cortex │ ├── brain_cortex_artificial_diverse_distinct_withboxplot.png │ ├── brain_cortex_artificial_diverse_overlap_withboxplot.png │ ├── brain_cortex_artificial_dominant_celltype_diverse_withboxplot.png │ ├── brain_cortex_artificial_dominant_rare_celltype_diverse_withboxplot.png │ ├── brain_cortex_artificial_missing_celltypes_visium_withboxplot.png │ ├── brain_cortex_artificial_partially_dominant_celltype_diverse_withboxplot.png │ ├── brain_cortex_artificial_regional_rare_celltype_diverse_withboxplot.png │ ├── brain_cortex_artificial_uniform_distinct_withboxplot.png │ └── brain_cortex_artificial_uniform_overlap_withboxplot.png │ ├── cerebellum_cell │ ├── cerebellum_cell_artificial_diverse_distinct_withboxplot.png │ ├── cerebellum_cell_artificial_diverse_overlap_withboxplot.png │ ├── cerebellum_cell_artificial_dominant_celltype_diverse_withboxplot.png │ ├── cerebellum_cell_artificial_dominant_rare_celltype_diverse_withboxplot.png │ ├── cerebellum_cell_artificial_missing_celltypes_visium_withboxplot.png │ ├── cerebellum_cell_artificial_partially_dominant_celltype_diverse_withboxplot.png │ ├── cerebellum_cell_artificial_regional_rare_celltype_diverse_withboxplot.png │ ├── cerebellum_cell_artificial_uniform_distinct_withboxplot.png │ └── cerebellum_cell_artificial_uniform_overlap_withboxplot.png │ ├── cerebellum_nucleus │ ├── cerebellum_nucleus_artificial_diverse_distinct_withboxplot.png │ ├── cerebellum_nucleus_artificial_diverse_overlap_withboxplot.png │ ├── cerebellum_nucleus_artificial_dominant_celltype_diverse_withboxplot.png │ ├── cerebellum_nucleus_artificial_dominant_rare_celltype_diverse_withboxplot.png │ ├── cerebellum_nucleus_artificial_missing_celltypes_visium_withboxplot.png │ ├── cerebellum_nucleus_artificial_partially_dominant_celltype_diverse_withboxplot.png │ ├── cerebellum_nucleus_artificial_regional_rare_celltype_diverse_withboxplot.png │ ├── cerebellum_nucleus_artificial_uniform_distinct_withboxplot.png │ └── cerebellum_nucleus_artificial_uniform_overlap_withboxplot.png │ ├── hippocampus │ ├── hippocampus_artificial_diverse_distinct_withboxplot.png │ ├── hippocampus_artificial_diverse_overlap_withboxplot.png │ ├── hippocampus_artificial_dominant_celltype_diverse_withboxplot.png │ ├── hippocampus_artificial_dominant_rare_celltype_diverse_withboxplot.png │ ├── hippocampus_artificial_missing_celltypes_visium_withboxplot.png │ ├── hippocampus_artificial_partially_dominant_celltype_diverse_withboxplot.png │ ├── hippocampus_artificial_regional_rare_celltype_diverse_withboxplot.png │ ├── hippocampus_artificial_uniform_distinct_withboxplot.png │ └── hippocampus_artificial_uniform_overlap_withboxplot.png │ ├── kidney │ ├── kidney_artificial_diverse_distinct_withboxplot.png │ ├── kidney_artificial_diverse_overlap_withboxplot.png │ ├── kidney_artificial_dominant_celltype_diverse_withboxplot.png │ ├── kidney_artificial_dominant_rare_celltype_diverse_withboxplot.png │ ├── kidney_artificial_missing_celltypes_visium_withboxplot.png │ ├── kidney_artificial_partially_dominant_celltype_diverse_withboxplot.png │ ├── kidney_artificial_regional_rare_celltype_diverse_withboxplot.png │ ├── kidney_artificial_uniform_distinct_withboxplot.png │ └── kidney_artificial_uniform_overlap_withboxplot.png │ └── scc_p5 │ ├── scc_p5_artificial_diverse_distinct_withboxplot.png │ ├── scc_p5_artificial_diverse_overlap_withboxplot.png │ ├── scc_p5_artificial_dominant_celltype_diverse_withboxplot.png │ ├── scc_p5_artificial_dominant_rare_celltype_diverse_withboxplot.png │ ├── scc_p5_artificial_missing_celltypes_visium_withboxplot.png │ ├── scc_p5_artificial_partially_dominant_celltype_diverse_withboxplot.png │ ├── scc_p5_artificial_regional_rare_celltype_diverse_withboxplot.png │ ├── scc_p5_artificial_uniform_distinct_withboxplot.png │ └── scc_p5_artificial_uniform_overlap_withboxplot.png ├── scripts ├── 0_init.R ├── 1a_run_gold_standard.txt ├── 1b_run_silver_standard.txt ├── 2a_calculate_reference_metric.R ├── 3a_evaluate_gold_standard_seqfish.R ├── 3b_evaluate_gold_standard_starmap.R ├── 3c_evaluate_silver_standard.R ├── 3d_evaluate_silver_standard_real.R ├── 3e_rare_celltypes_detection.R ├── 4a_combine_silver_gold_plots.R ├── 4b_plot_prcurves_dominant_vs_others.R ├── 4c_plot_funky_heatmap.R ├── 5a_create_pseudosamples_music.R ├── 5b_compare_method_parameters.R ├── 5c_compare_method_parameters_real.R ├── ex_plot_gold_standard_proportions.R ├── ex_plot_liver_and_melanoma.R ├── ex_plot_runtime_scalability.R ├── ex_plot_silver_standard_UMAP.R ├── liver_analysis │ ├── 1_preprocess_liver_ref.R │ ├── 2_run_liver_dataset.txt │ ├── 3a_evaluate_liver_visium.R │ ├── 3b_evaluate_synthetic_liver.R │ └── ex_figure1d.R ├── melanoma_analysis │ ├── 1_preprocess_melanoma_visium.R │ ├── 2_run_melanoma_visium.txt │ └── 3_evaluate_melanoma_visium.R ├── preprocess_gold_standard_datasets │ ├── 1a_preprocess_gold_standard_seqfish.R │ └── 1b_preprocess_gold_standard_STARMAP.R ├── preprocess_silver_standard_sc_datasets │ ├── 1a-process_brain_cortex.R │ ├── 1b-process_cerebellum.R │ ├── 1c-process_hippocampus.R │ ├── 1d-process_kidney.R │ ├── 1e-process_scc_p5.R │ ├── 1f-process_melanoma.R │ ├── 2a-standardize_all_datasets.R │ └── 2b-statistics_scrnaseq_datasets.R ├── reference_sensitivity_analysis │ ├── 1_create_extra_reference_brain.R │ ├── 2_run_sensitivity_analysis.txt │ └── 3_evaluate_sensitivity.R ├── runtime │ ├── 1_runtime_analysis.txt │ └── 2_plot_runtimes.R └── scalability_analysis │ ├── 1_downsample_datasets.R │ ├── 2_run_scalability_analysis.txt │ └── 3_plot_scalability_heatmap.R ├── spotless-benchmark.Rproj ├── standards ├── dataset_properties.xlsx └── standard.config ├── subworkflows ├── data_generation │ ├── generate_data.nf │ └── generate_synthetic_data.R ├── deconvolution │ ├── README.md │ ├── cell2location │ │ ├── Dockerfile │ │ ├── build_model.py │ │ ├── environment.yml │ │ ├── fit_model.py │ │ └── run_method.nf │ ├── convertBetweenRDSandH5AD.R │ ├── destvi │ │ ├── Dockerfile │ │ ├── build_model.py │ │ ├── fit_model.py │ │ └── run_method.nf │ ├── downsampleMatrix.R │ ├── dstg │ │ ├── Dockerfile │ │ ├── convertSeuratToMatrix.R │ │ ├── run_method.nf │ │ └── test_spot_fun.R │ ├── music │ │ ├── Dockerfile │ │ ├── run_method.nf │ │ └── script_nf.R │ ├── nnls │ │ ├── Dockerfile │ │ ├── run_method.nf │ │ └── script_nf.R │ ├── rctd │ │ ├── Dockerfile │ │ ├── run_method.nf │ │ └── script_nf.R │ ├── run_methods.nf │ ├── seurat │ │ ├── run_method.nf │ │ └── script_nf.R │ ├── spatialdwls │ │ ├── Dockerfile │ │ ├── requirements.txt │ │ ├── run_method.nf │ │ └── script_nf.R │ ├── spotlight │ │ ├── Dockerfile │ │ ├── run_method.nf │ │ └── script_nf.R │ ├── stereoscope │ │ ├── Dockerfile │ │ ├── compute_HVGs.py │ │ ├── environment.yml │ │ └── run_method.nf │ ├── stride │ │ ├── Dockerfile │ │ ├── README.md │ │ ├── createFiles.py │ │ ├── extra_code.txt │ │ ├── fit_stride.nf │ │ ├── identify_markers.py │ │ └── run_method.nf │ └── tangram │ │ ├── Dockerfile │ │ ├── environment.yml │ │ ├── getCellComposition.R │ │ ├── run_method.nf │ │ └── script_nf.py ├── evaluation │ ├── Dockerfile │ ├── evaluate_methods.nf │ └── metrics.R ├── helper_processes.nf └── test_nf.nf └── unit-test ├── notes.txt ├── test_generate_data.R ├── test_run_dataset.R ├── test_run_dataset ├── metrics_cell2location_test_sp_data ├── metrics_destvi_test_sp_data ├── metrics_dstg_test_sp_data ├── metrics_music_test_sp_data ├── metrics_nnls_test_sp_data ├── metrics_rctd_test_sp_data ├── metrics_seurat_test_sp_data ├── metrics_spatialdwls_test_sp_data ├── metrics_spotlight_test_sp_data ├── metrics_stereoscope_test_sp_data ├── metrics_stride_test_sp_data ├── metrics_tangram_test_sp_data ├── proportions_cell2location_test_sp_data ├── proportions_destvi_test_sp_data ├── proportions_dstg_test_sp_data ├── proportions_music_test_sp_data ├── proportions_nnls_test_sp_data ├── proportions_rctd_test_sp_data ├── proportions_seurat_test_sp_data ├── proportions_spatialdwls_test_sp_data ├── proportions_spotlight_test_sp_data ├── proportions_stereoscope_test_sp_data ├── proportions_stride_test_sp_data └── proportions_tangram_test_sp_data ├── test_sc_data.rds └── test_sp_data.rds /.gitattributes: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/saeyslab/spotless-benchmark/HEAD/.gitattributes -------------------------------------------------------------------------------- /.github/workflows/test_generate_dataset.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/saeyslab/spotless-benchmark/HEAD/.github/workflows/test_generate_dataset.yml -------------------------------------------------------------------------------- /.github/workflows/test_run_dataset_R.yml: 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