├── Benchmarking-Integration-Methods ├── 1-run_harmony.R ├── 2-run_scanorama.py ├── 3-compute_lisi.R ├── 4-plot_lisi.R ├── 5-cluster_harmony.R ├── 6-cluster_scanorama.py └── 7-plot_umaps.R ├── Integration ├── 10_filter_annotate.R ├── 1_process_gene_names_objects.R ├── 2_find_batch_specific_genes.R ├── 3_normalize_each_dataset.R ├── 4_find_integration_features.R ├── 5_scale_each_dataset.R ├── 6_find_integration_anchors.R ├── 7_integration.R ├── 8_process_integrated_obj.R ├── 9_cluster_atlas.R └── README.md ├── Patient stratification ├── 1_create_proportions_dataset.R ├── 2_cluster_patients.R ├── 3_random_forest.R └── README.md ├── Projections ├── README.md ├── atlas_projection.Rmd ├── cancer_subtype_palette.rds └── cell_type_palette.rds ├── README.md ├── Random Forest ├── 1-calculate_cell_type_signatures.R ├── 2-create_test_sets_for_cross_validation.R ├── 3-run_random_forest.R ├── 4-evaluate_performance.R ├── 5-plot_figures.R ├── README.md └── data │ └── supp_table_2.xlsx ├── ST-breast ├── 1-10x_breast_QC.Rmd ├── 2-10x_breast_GO_enrichment.Rmd ├── 3-10x_breast_immune_reference.Rmd ├── 4-10x_breast_stratification.Rmd ├── RCTD-10x_breast_immune_reference.Rmd ├── RCTD-SPOTlight_comparison.Rmd └── README.md ├── ST-oropharyngeal ├── 1-australia_oroph_processing.Rmd ├── 2-australia_oroph_biological.Rmd ├── 3-australia_oroph_deconv.Rmd ├── 4-australia_oro_stratification.Rmd ├── 6-australia_oro_digitalFISH.Rmd ├── RCTD-SPOTlight_comparison.Rmd ├── RCTD-australia_oroph_deconv.Rmd ├── README.md ├── make_oroph_deconv.cmd └── spotlight_deconv_oroph_job.R ├── misc ├── SPOTlight_deconvolution_job.R ├── atlas.png ├── col_df_scrpt.R └── paths.R └── utils ├── bin.r ├── process_gene_names.R └── spatial_plot_spaniel.R /Benchmarking-Integration-Methods/1-run_harmony.R: -------------------------------------------------------------------------------- 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