├── .gitignore ├── 01_purity_levels_experiment ├── exclude_normal_epithelial │ ├── 02_generate_metadata.ipynb │ ├── 02_smote.pbs │ ├── 04_1_seurat_individual_patient.pbs │ ├── 07_simulate_test_mixtures.pbs │ ├── 07_simulate_train_mixtures.pbs │ ├── 08_concatenate_test_adata_objects.pbs │ ├── 08_concatenate_train_adata_objects.pbs │ ├── 9_1_prepare_method_specific_data.ipynb │ ├── 9_2_run_bisque.pbs │ ├── 9_2_run_bprism.pbs │ ├── 9_2_run_cbx.pbs │ ├── 9_2_run_cpm_1.pbs │ ├── 9_2_run_cpm_2.pbs │ ├── 9_2_run_dwls_1.pbs │ ├── 9_2_run_dwls_2.pbs │ ├── 9_2_run_dwls_all.pbs │ ├── 9_2_run_epic.pbs │ ├── 9_2_run_hspe.pbs │ ├── 9_2_run_music.pbs │ ├── 9_2_run_scaden.pbs │ ├── 9_3_collate_test_results.ipynb │ └── data │ │ └── Whole_miniatlas_meta_no_normal.csv └── include_normal_epithelial │ ├── 02_generate_metadata.ipynb │ ├── 02_smote.pbs │ ├── 04_1_seurat_individual_patient.pbs │ ├── 05_investigate_smoted_umap.ipynb │ ├── 07_simulate_test_mixtures.pbs │ ├── 07_simulate_train_mixtures.pbs │ ├── 08_concatenate_test_adata_objects.pbs │ ├── 08_concatenate_train_adata_objects.pbs │ ├── 9_1_prepare_method_specific_data.ipynb │ ├── 9_2_run_bisque.pbs │ ├── 9_2_run_bprism.pbs │ ├── 9_2_run_cbx.pbs │ ├── 9_2_run_cpm_1.pbs │ ├── 9_2_run_cpm_2.pbs │ ├── 9_2_run_dwls_1.pbs │ ├── 9_2_run_dwls_2.pbs │ ├── 9_2_run_dwls_all.pbs │ ├── 9_2_run_epic.pbs │ ├── 9_2_run_hspe.pbs │ ├── 9_2_run_music.pbs │ ├── 9_2_run_scaden.pbs │ ├── 9_3_collate_test_results.ipynb │ └── data │ └── Whole_miniatlas_meta_9_10.csv ├── 02_normal_epithelial_lineages_experiment ├── 02_generate_metadata.ipynb ├── 02_smote.pbs ├── 02_smote.py ├── 03_transpose_smoted_data.pbs ├── 03_transpose_smoted_data.py ├── 04_1_seurat_individual_patient.R ├── 04_1_seurat_individual_patient.pbs ├── 07_simulate_test_mixtures.pbs ├── 07_simulate_test_mixtures.py ├── 07_simulate_train_mixtures.pbs ├── 07_simulate_train_mixtures_kondrashova.py ├── 08_concatenate_test_adata_objects.pbs ├── 08_concatenate_test_adata_objects.py ├── 08_concatenate_train_adata_objects.pbs ├── 08_concatenate_train_adata_objects.py ├── 9_1_prepare_method_specific_data.ipynb ├── 9_2_run_bisque.pbs ├── 9_2_run_bprism.pbs ├── 9_2_run_cbx.pbs ├── 9_2_run_cpm_1.pbs ├── 9_2_run_cpm_2.pbs ├── 9_2_run_dwls_1.pbs ├── 9_2_run_dwls_2.pbs ├── 9_2_run_dwls_all.pbs ├── 9_2_run_epic.pbs ├── 9_2_run_hspe.pbs ├── 9_2_run_music.pbs ├── 9_2_run_scaden.pbs ├── 9_3_collate_test_results.ipynb └── data │ ├── Whole_miniatlas_meta_minor_immune_lineages.csv │ └── Whole_miniatlas_meta_normal_lineages.csv ├── 03_immune_lineages_experiment ├── minor_level │ ├── 02_generate_metadata.ipynb │ ├── 02_smote.pbs │ ├── 07_simulate_test_mixtures.pbs │ ├── 07_simulate_train_mixtures.pbs │ ├── 08_concatenate_test_adata_objects.pbs │ ├── 08_concatenate_train_adata_objects.pbs │ ├── 9_1_prepare_method_specific_data.ipynb │ ├── 9_2_run_bisque.pbs │ ├── 9_2_run_bprism.pbs │ ├── 9_2_run_cbx.pbs │ ├── 9_2_run_cpm_1.pbs │ ├── 9_2_run_cpm_2.pbs │ ├── 9_2_run_dwls_1.pbs │ ├── 9_2_run_dwls_2.pbs │ ├── 9_2_run_dwls_all.pbs │ ├── 9_2_run_epic.pbs │ ├── 9_2_run_hspe.pbs │ ├── 9_2_run_music.pbs │ ├── 9_2_run_scaden.pbs │ ├── 9_3_collate_test_results.ipynb │ └── data │ │ └── Whole_miniatlas_meta_minor_immune_lineages.csv └── subset_level │ ├── 02_generate_metadata.ipynb │ ├── 02_smote.pbs │ ├── 07_simulate_test_mixtures.pbs │ ├── 07_simulate_train_mixtures.pbs │ ├── 08_concatenate_test_adata_objects.pbs │ ├── 08_concatenate_train_adata_objects.pbs │ ├── 9_1_prepare_method_specific_data.ipynb │ ├── 9_2_run_bisque.pbs │ ├── 9_2_run_bprism.pbs │ ├── 9_2_run_cbx.pbs │ ├── 9_2_run_cpm_1.pbs │ ├── 9_2_run_cpm_2.pbs │ ├── 9_2_run_dwls_1.pbs │ ├── 9_2_run_dwls_2.pbs │ ├── 9_2_run_dwls_all.pbs │ ├── 9_2_run_epic.pbs │ ├── 9_2_run_hspe.pbs │ ├── 9_2_run_music.pbs │ ├── 9_2_run_scaden.pbs │ ├── 9_3_collate_test_results.ipynb │ └── data │ └── Whole_miniatlas_meta_immune_lineages_remastered.csv ├── 04_tcga_bulk_validation ├── 0_collect_raw_counts.ipynb ├── 10_validation.ipynb ├── 9_1_prepare_tool_specific_data.ipynb ├── 9_2_run_bisque.pbs ├── 9_2_run_bprism.pbs ├── 9_2_run_cbx.pbs ├── 9_2_run_cpm_1.pbs ├── 9_2_run_cpm_2.pbs ├── 9_2_run_dwls_1.pbs ├── 9_2_run_dwls_2.pbs ├── 9_2_run_epic.pbs ├── 9_2_run_hspe.pbs ├── 9_2_run_music.pbs ├── 9_2_run_scaden.pbs ├── 9_3_collate_test_results.ipynb └── data │ └── Whole_miniatlas_meta_9_10.csv ├── 05_external_scrna_validation ├── bassez_et_al │ ├── 00_cell_counts_analysis.ipynb │ ├── 00_consolidate_immune_lineages.ipynb │ ├── 01_normalize_raw_counts.R │ ├── 01_normalize_raw_counts.ipynb │ ├── 02_generate_metadata.ipynb │ ├── 02_smote.pbs │ ├── 04_1_seurat_individual_patient.pbs │ ├── 05_investigate_smoted_umap.ipynb │ ├── 07_simulate_test_mixtures.pbs │ ├── 07_simulate_train_mixtures.pbs │ ├── 9_1_prepare_tool_specific_data.ipynb │ ├── 9_2_run_bisque.pbs │ ├── 9_2_run_bprism.pbs │ ├── 9_2_run_cbx.pbs │ ├── 9_2_run_dwls_1.pbs │ ├── 9_2_run_dwls_2.pbs │ ├── 9_2_run_epic.pbs │ ├── 9_2_run_hspe.pbs │ ├── 9_2_run_music.pbs │ ├── 9_2_run_scaden.pbs │ ├── 9_3_collate_test_results.ipynb │ └── data │ │ └── Miniatlas_meta_9_10.tsv └── pal_et_al │ ├── 00_consolidate_cell_annotations.ipynb │ ├── 01_normalize_raw_counts.ipynb │ ├── 02_generate_metadata.ipynb │ ├── 02_smote.pbs │ ├── 04_1_seurat_individual_patient.pbs │ ├── 05_qa_smote_cells.ipynb │ ├── 06_filter_smoted_counts.pbs │ ├── 07_simulate_test_mixtures.pbs │ ├── 07_simulate_train_mixtures.pbs │ ├── 09_1_prepare_tool_specific_data.ipynb │ ├── 09_2_run_bisque.pbs │ ├── 09_2_run_bprism.pbs │ ├── 09_2_run_cbx.pbs │ ├── 09_2_run_dwls_1.pbs │ ├── 09_2_run_dwls_2.pbs │ ├── 09_2_run_epic.pbs │ ├── 09_2_run_hspe.pbs │ ├── 09_2_run_music.pbs │ ├── 09_2_run_scaden.pbs │ ├── 09_3_collate_test_results.ipynb │ └── data │ └── Miniatlas_meta_major.tsv ├── 06_batch_effect_validation ├── bassez_et_al │ ├── 00_consolidate_immune_lineages.ipynb │ ├── 02_generate_metadata.ipynb │ ├── 02_smote.pbs │ ├── 04_1_seurat_individual_patient.pbs │ ├── 05_investigate_smoted_umap.ipynb │ ├── 07_simulate_test_mixtures.pbs │ ├── 09_1_prepare_tool_specific_data.ipynb │ ├── 09_2_run_bisque.pbs │ ├── 09_2_run_bprism_v2.pbs │ ├── 09_2_run_cbx.pbs │ ├── 09_2_run_dwls_1.pbs │ ├── 09_2_run_dwls_2.pbs │ ├── 09_2_run_epic.pbs │ ├── 09_2_run_hspe.pbs │ ├── 09_2_run_music.pbs │ ├── 09_2_run_scaden.pbs │ ├── 09_3_collate_test_results.ipynb │ └── data │ │ └── Miniatlas_major_immune_lineage.tsv └── pal_et_al │ ├── 00_consolidate_cell_annotations.ipynb │ ├── 02_generate_metadata.ipynb │ ├── 02_smote.pbs │ ├── 04_1_seurat_individual_patient.pbs │ ├── 07_simulate_test_mixtures.pbs │ ├── 09_1_prepare_tool_specific_data.ipynb │ ├── 09_2_run_bisque.pbs │ ├── 09_2_run_bprism_v2.pbs │ ├── 09_2_run_cbx.pbs │ ├── 09_2_run_dwls_1.pbs │ ├── 09_2_run_dwls_2.pbs │ ├── 09_2_run_epic.pbs │ ├── 09_2_run_hspe.pbs │ ├── 09_2_run_music.pbs │ ├── 09_2_run_scaden.pbs │ ├── 09_3_collate_test_results.ipynb │ └── data │ └── Miniatlas_major_immune_lineage.tsv ├── CITATION.cff ├── LICENSE ├── README.md ├── params ├── README.md ├── sample_input_file.csv ├── seurat_CCA_params_file.csv ├── seurat_gene_input_file.csv └── seurat_params_file.csv ├── src ├── 02_smote.py ├── 03_transpose_smoted_data.py ├── 04_1_seurat_individual_patient.R ├── 04_2_seurat_integration.R ├── 06_filter_smoted_counts.py ├── 07_simulate_test_mixtures.py ├── 07_simulate_train_menden_et_al_method.py ├── 07_simulate_train_mixtures_sparse_method.py ├── 08_concatenate_test_adata_objects.py ├── 08_concatenate_train_adata_objects.py ├── 9_2_run_bisque.R ├── 9_2_run_bprism.R ├── 9_2_run_cpm.R ├── 9_2_run_cpm_1.R ├── 9_2_run_cpm_2.R ├── 9_2_run_dwls_1.R ├── 9_2_run_dwls_2.R ├── 9_2_run_dwls_all.R ├── 9_2_run_epic.R ├── 9_2_run_hspe.R ├── 9_2_run_music.R └── utils │ ├── 1_CPM_functions.R │ ├── 1_DWLS_de_analysis.R │ ├── 1_DWLS_deconvolution.R │ └── 1_DWLS_functions.R └── visualizations ├── README.md ├── main_fig_2_a_b.ipynb ├── main_fig_2_c_d.ipynb ├── main_fig_3.ipynb ├── main_fig_4a.ipynb ├── main_fig_4b_c.ipynb ├── main_fig_5_b_c.ipynb ├── main_fig_5a_d_e.ipynb ├── supplementary_fig_10a_b.ipynb ├── supplementary_fig_10c_d.ipynb ├── supplementary_fig_12.ipynb ├── supplementary_fig_13.ipynb ├── supplementary_fig_14.ipynb ├── supplementary_fig_15.ipynb ├── supplementary_fig_16.ipynb ├── supplementary_fig_17a_b.ipynb ├── supplementary_fig_17c_d.ipynb ├── supplementary_fig_17e_f.ipynb ├── supplementary_fig_18.ipynb ├── supplementary_fig_1a_c_e.ipynb ├── supplementary_fig_1b_d_f.ipynb ├── supplementary_fig_2.ipynb ├── supplementary_fig_3.ipynb ├── supplementary_fig_4_11.ipynb ├── supplementary_fig_5.ipynb ├── supplementary_fig_6.ipynb ├── supplementary_fig_7a_b_8a.ipynb ├── supplementary_fig_7c_d_8b.ipynb └── supplementary_fig_9.ipynb /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/.gitignore -------------------------------------------------------------------------------- /01_purity_levels_experiment/exclude_normal_epithelial/02_generate_metadata.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/01_purity_levels_experiment/exclude_normal_epithelial/02_generate_metadata.ipynb -------------------------------------------------------------------------------- /01_purity_levels_experiment/exclude_normal_epithelial/02_smote.pbs: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/01_purity_levels_experiment/exclude_normal_epithelial/02_smote.pbs -------------------------------------------------------------------------------- /01_purity_levels_experiment/exclude_normal_epithelial/04_1_seurat_individual_patient.pbs: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/01_purity_levels_experiment/exclude_normal_epithelial/04_1_seurat_individual_patient.pbs -------------------------------------------------------------------------------- /01_purity_levels_experiment/exclude_normal_epithelial/07_simulate_test_mixtures.pbs: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/01_purity_levels_experiment/exclude_normal_epithelial/07_simulate_test_mixtures.pbs -------------------------------------------------------------------------------- /01_purity_levels_experiment/exclude_normal_epithelial/07_simulate_train_mixtures.pbs: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/01_purity_levels_experiment/exclude_normal_epithelial/07_simulate_train_mixtures.pbs -------------------------------------------------------------------------------- /01_purity_levels_experiment/exclude_normal_epithelial/08_concatenate_test_adata_objects.pbs: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/01_purity_levels_experiment/exclude_normal_epithelial/08_concatenate_test_adata_objects.pbs -------------------------------------------------------------------------------- /01_purity_levels_experiment/exclude_normal_epithelial/08_concatenate_train_adata_objects.pbs: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/01_purity_levels_experiment/exclude_normal_epithelial/08_concatenate_train_adata_objects.pbs -------------------------------------------------------------------------------- /01_purity_levels_experiment/exclude_normal_epithelial/9_1_prepare_method_specific_data.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/01_purity_levels_experiment/exclude_normal_epithelial/9_1_prepare_method_specific_data.ipynb -------------------------------------------------------------------------------- /01_purity_levels_experiment/exclude_normal_epithelial/9_2_run_bisque.pbs: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/01_purity_levels_experiment/exclude_normal_epithelial/9_2_run_bisque.pbs -------------------------------------------------------------------------------- /01_purity_levels_experiment/exclude_normal_epithelial/9_2_run_bprism.pbs: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/01_purity_levels_experiment/exclude_normal_epithelial/9_2_run_bprism.pbs -------------------------------------------------------------------------------- /01_purity_levels_experiment/exclude_normal_epithelial/9_2_run_cbx.pbs: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/01_purity_levels_experiment/exclude_normal_epithelial/9_2_run_cbx.pbs -------------------------------------------------------------------------------- /01_purity_levels_experiment/exclude_normal_epithelial/9_2_run_cpm_1.pbs: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/01_purity_levels_experiment/exclude_normal_epithelial/9_2_run_cpm_1.pbs -------------------------------------------------------------------------------- /01_purity_levels_experiment/exclude_normal_epithelial/9_2_run_cpm_2.pbs: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/01_purity_levels_experiment/exclude_normal_epithelial/9_2_run_cpm_2.pbs -------------------------------------------------------------------------------- /01_purity_levels_experiment/exclude_normal_epithelial/9_2_run_dwls_1.pbs: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/01_purity_levels_experiment/exclude_normal_epithelial/9_2_run_dwls_1.pbs -------------------------------------------------------------------------------- /01_purity_levels_experiment/exclude_normal_epithelial/9_2_run_dwls_2.pbs: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/01_purity_levels_experiment/exclude_normal_epithelial/9_2_run_dwls_2.pbs -------------------------------------------------------------------------------- /01_purity_levels_experiment/exclude_normal_epithelial/9_2_run_dwls_all.pbs: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/01_purity_levels_experiment/exclude_normal_epithelial/9_2_run_dwls_all.pbs -------------------------------------------------------------------------------- /01_purity_levels_experiment/exclude_normal_epithelial/9_2_run_epic.pbs: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/01_purity_levels_experiment/exclude_normal_epithelial/9_2_run_epic.pbs -------------------------------------------------------------------------------- /01_purity_levels_experiment/exclude_normal_epithelial/9_2_run_hspe.pbs: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/01_purity_levels_experiment/exclude_normal_epithelial/9_2_run_hspe.pbs -------------------------------------------------------------------------------- /01_purity_levels_experiment/exclude_normal_epithelial/9_2_run_music.pbs: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/01_purity_levels_experiment/exclude_normal_epithelial/9_2_run_music.pbs -------------------------------------------------------------------------------- /01_purity_levels_experiment/exclude_normal_epithelial/9_2_run_scaden.pbs: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/01_purity_levels_experiment/exclude_normal_epithelial/9_2_run_scaden.pbs -------------------------------------------------------------------------------- /01_purity_levels_experiment/exclude_normal_epithelial/9_3_collate_test_results.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/01_purity_levels_experiment/exclude_normal_epithelial/9_3_collate_test_results.ipynb -------------------------------------------------------------------------------- /01_purity_levels_experiment/exclude_normal_epithelial/data/Whole_miniatlas_meta_no_normal.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/01_purity_levels_experiment/exclude_normal_epithelial/data/Whole_miniatlas_meta_no_normal.csv -------------------------------------------------------------------------------- /01_purity_levels_experiment/include_normal_epithelial/02_generate_metadata.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/01_purity_levels_experiment/include_normal_epithelial/02_generate_metadata.ipynb -------------------------------------------------------------------------------- /01_purity_levels_experiment/include_normal_epithelial/02_smote.pbs: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/01_purity_levels_experiment/include_normal_epithelial/02_smote.pbs -------------------------------------------------------------------------------- /01_purity_levels_experiment/include_normal_epithelial/04_1_seurat_individual_patient.pbs: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/01_purity_levels_experiment/include_normal_epithelial/04_1_seurat_individual_patient.pbs -------------------------------------------------------------------------------- /01_purity_levels_experiment/include_normal_epithelial/05_investigate_smoted_umap.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/01_purity_levels_experiment/include_normal_epithelial/05_investigate_smoted_umap.ipynb -------------------------------------------------------------------------------- /01_purity_levels_experiment/include_normal_epithelial/07_simulate_test_mixtures.pbs: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/01_purity_levels_experiment/include_normal_epithelial/07_simulate_test_mixtures.pbs -------------------------------------------------------------------------------- /01_purity_levels_experiment/include_normal_epithelial/07_simulate_train_mixtures.pbs: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/01_purity_levels_experiment/include_normal_epithelial/07_simulate_train_mixtures.pbs -------------------------------------------------------------------------------- /01_purity_levels_experiment/include_normal_epithelial/08_concatenate_test_adata_objects.pbs: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/01_purity_levels_experiment/include_normal_epithelial/08_concatenate_test_adata_objects.pbs -------------------------------------------------------------------------------- /01_purity_levels_experiment/include_normal_epithelial/08_concatenate_train_adata_objects.pbs: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/01_purity_levels_experiment/include_normal_epithelial/08_concatenate_train_adata_objects.pbs -------------------------------------------------------------------------------- /01_purity_levels_experiment/include_normal_epithelial/9_1_prepare_method_specific_data.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/01_purity_levels_experiment/include_normal_epithelial/9_1_prepare_method_specific_data.ipynb -------------------------------------------------------------------------------- /01_purity_levels_experiment/include_normal_epithelial/9_2_run_bisque.pbs: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/01_purity_levels_experiment/include_normal_epithelial/9_2_run_bisque.pbs -------------------------------------------------------------------------------- /01_purity_levels_experiment/include_normal_epithelial/9_2_run_bprism.pbs: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/01_purity_levels_experiment/include_normal_epithelial/9_2_run_bprism.pbs -------------------------------------------------------------------------------- /01_purity_levels_experiment/include_normal_epithelial/9_2_run_cbx.pbs: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/01_purity_levels_experiment/include_normal_epithelial/9_2_run_cbx.pbs -------------------------------------------------------------------------------- /01_purity_levels_experiment/include_normal_epithelial/9_2_run_cpm_1.pbs: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/01_purity_levels_experiment/include_normal_epithelial/9_2_run_cpm_1.pbs -------------------------------------------------------------------------------- /01_purity_levels_experiment/include_normal_epithelial/9_2_run_cpm_2.pbs: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/01_purity_levels_experiment/include_normal_epithelial/9_2_run_cpm_2.pbs -------------------------------------------------------------------------------- /01_purity_levels_experiment/include_normal_epithelial/9_2_run_dwls_1.pbs: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/01_purity_levels_experiment/include_normal_epithelial/9_2_run_dwls_1.pbs -------------------------------------------------------------------------------- /01_purity_levels_experiment/include_normal_epithelial/9_2_run_dwls_2.pbs: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/01_purity_levels_experiment/include_normal_epithelial/9_2_run_dwls_2.pbs -------------------------------------------------------------------------------- /01_purity_levels_experiment/include_normal_epithelial/9_2_run_dwls_all.pbs: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/01_purity_levels_experiment/include_normal_epithelial/9_2_run_dwls_all.pbs -------------------------------------------------------------------------------- /01_purity_levels_experiment/include_normal_epithelial/9_2_run_epic.pbs: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/01_purity_levels_experiment/include_normal_epithelial/9_2_run_epic.pbs -------------------------------------------------------------------------------- /01_purity_levels_experiment/include_normal_epithelial/9_2_run_hspe.pbs: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/01_purity_levels_experiment/include_normal_epithelial/9_2_run_hspe.pbs -------------------------------------------------------------------------------- /01_purity_levels_experiment/include_normal_epithelial/9_2_run_music.pbs: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/01_purity_levels_experiment/include_normal_epithelial/9_2_run_music.pbs -------------------------------------------------------------------------------- /01_purity_levels_experiment/include_normal_epithelial/9_2_run_scaden.pbs: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/01_purity_levels_experiment/include_normal_epithelial/9_2_run_scaden.pbs -------------------------------------------------------------------------------- /01_purity_levels_experiment/include_normal_epithelial/9_3_collate_test_results.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/01_purity_levels_experiment/include_normal_epithelial/9_3_collate_test_results.ipynb -------------------------------------------------------------------------------- /01_purity_levels_experiment/include_normal_epithelial/data/Whole_miniatlas_meta_9_10.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/01_purity_levels_experiment/include_normal_epithelial/data/Whole_miniatlas_meta_9_10.csv -------------------------------------------------------------------------------- /02_normal_epithelial_lineages_experiment/02_generate_metadata.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/02_normal_epithelial_lineages_experiment/02_generate_metadata.ipynb -------------------------------------------------------------------------------- /02_normal_epithelial_lineages_experiment/02_smote.pbs: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/02_normal_epithelial_lineages_experiment/02_smote.pbs -------------------------------------------------------------------------------- /02_normal_epithelial_lineages_experiment/02_smote.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/02_normal_epithelial_lineages_experiment/02_smote.py -------------------------------------------------------------------------------- /02_normal_epithelial_lineages_experiment/03_transpose_smoted_data.pbs: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/02_normal_epithelial_lineages_experiment/03_transpose_smoted_data.pbs -------------------------------------------------------------------------------- /02_normal_epithelial_lineages_experiment/03_transpose_smoted_data.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/02_normal_epithelial_lineages_experiment/03_transpose_smoted_data.py -------------------------------------------------------------------------------- /02_normal_epithelial_lineages_experiment/04_1_seurat_individual_patient.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/02_normal_epithelial_lineages_experiment/04_1_seurat_individual_patient.R -------------------------------------------------------------------------------- /02_normal_epithelial_lineages_experiment/04_1_seurat_individual_patient.pbs: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/02_normal_epithelial_lineages_experiment/04_1_seurat_individual_patient.pbs -------------------------------------------------------------------------------- /02_normal_epithelial_lineages_experiment/07_simulate_test_mixtures.pbs: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/02_normal_epithelial_lineages_experiment/07_simulate_test_mixtures.pbs -------------------------------------------------------------------------------- /02_normal_epithelial_lineages_experiment/07_simulate_test_mixtures.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/02_normal_epithelial_lineages_experiment/07_simulate_test_mixtures.py -------------------------------------------------------------------------------- /02_normal_epithelial_lineages_experiment/07_simulate_train_mixtures.pbs: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/02_normal_epithelial_lineages_experiment/07_simulate_train_mixtures.pbs -------------------------------------------------------------------------------- /02_normal_epithelial_lineages_experiment/07_simulate_train_mixtures_kondrashova.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/02_normal_epithelial_lineages_experiment/07_simulate_train_mixtures_kondrashova.py -------------------------------------------------------------------------------- /02_normal_epithelial_lineages_experiment/08_concatenate_test_adata_objects.pbs: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/02_normal_epithelial_lineages_experiment/08_concatenate_test_adata_objects.pbs -------------------------------------------------------------------------------- /02_normal_epithelial_lineages_experiment/08_concatenate_test_adata_objects.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/02_normal_epithelial_lineages_experiment/08_concatenate_test_adata_objects.py -------------------------------------------------------------------------------- /02_normal_epithelial_lineages_experiment/08_concatenate_train_adata_objects.pbs: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/02_normal_epithelial_lineages_experiment/08_concatenate_train_adata_objects.pbs -------------------------------------------------------------------------------- /02_normal_epithelial_lineages_experiment/08_concatenate_train_adata_objects.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/02_normal_epithelial_lineages_experiment/08_concatenate_train_adata_objects.py -------------------------------------------------------------------------------- /02_normal_epithelial_lineages_experiment/9_1_prepare_method_specific_data.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/02_normal_epithelial_lineages_experiment/9_1_prepare_method_specific_data.ipynb -------------------------------------------------------------------------------- /02_normal_epithelial_lineages_experiment/9_2_run_bisque.pbs: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/02_normal_epithelial_lineages_experiment/9_2_run_bisque.pbs -------------------------------------------------------------------------------- /02_normal_epithelial_lineages_experiment/9_2_run_bprism.pbs: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/02_normal_epithelial_lineages_experiment/9_2_run_bprism.pbs -------------------------------------------------------------------------------- /02_normal_epithelial_lineages_experiment/9_2_run_cbx.pbs: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/02_normal_epithelial_lineages_experiment/9_2_run_cbx.pbs -------------------------------------------------------------------------------- /02_normal_epithelial_lineages_experiment/9_2_run_cpm_1.pbs: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/02_normal_epithelial_lineages_experiment/9_2_run_cpm_1.pbs -------------------------------------------------------------------------------- /02_normal_epithelial_lineages_experiment/9_2_run_cpm_2.pbs: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/02_normal_epithelial_lineages_experiment/9_2_run_cpm_2.pbs -------------------------------------------------------------------------------- /02_normal_epithelial_lineages_experiment/9_2_run_dwls_1.pbs: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/02_normal_epithelial_lineages_experiment/9_2_run_dwls_1.pbs -------------------------------------------------------------------------------- /02_normal_epithelial_lineages_experiment/9_2_run_dwls_2.pbs: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/02_normal_epithelial_lineages_experiment/9_2_run_dwls_2.pbs -------------------------------------------------------------------------------- /02_normal_epithelial_lineages_experiment/9_2_run_dwls_all.pbs: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/02_normal_epithelial_lineages_experiment/9_2_run_dwls_all.pbs -------------------------------------------------------------------------------- /02_normal_epithelial_lineages_experiment/9_2_run_epic.pbs: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/02_normal_epithelial_lineages_experiment/9_2_run_epic.pbs -------------------------------------------------------------------------------- /02_normal_epithelial_lineages_experiment/9_2_run_hspe.pbs: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/02_normal_epithelial_lineages_experiment/9_2_run_hspe.pbs -------------------------------------------------------------------------------- /02_normal_epithelial_lineages_experiment/9_2_run_music.pbs: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/02_normal_epithelial_lineages_experiment/9_2_run_music.pbs -------------------------------------------------------------------------------- /02_normal_epithelial_lineages_experiment/9_2_run_scaden.pbs: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/02_normal_epithelial_lineages_experiment/9_2_run_scaden.pbs -------------------------------------------------------------------------------- /02_normal_epithelial_lineages_experiment/9_3_collate_test_results.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/02_normal_epithelial_lineages_experiment/9_3_collate_test_results.ipynb -------------------------------------------------------------------------------- /02_normal_epithelial_lineages_experiment/data/Whole_miniatlas_meta_minor_immune_lineages.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/02_normal_epithelial_lineages_experiment/data/Whole_miniatlas_meta_minor_immune_lineages.csv -------------------------------------------------------------------------------- /02_normal_epithelial_lineages_experiment/data/Whole_miniatlas_meta_normal_lineages.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/02_normal_epithelial_lineages_experiment/data/Whole_miniatlas_meta_normal_lineages.csv -------------------------------------------------------------------------------- /03_immune_lineages_experiment/minor_level/02_generate_metadata.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/03_immune_lineages_experiment/minor_level/02_generate_metadata.ipynb -------------------------------------------------------------------------------- /03_immune_lineages_experiment/minor_level/02_smote.pbs: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/03_immune_lineages_experiment/minor_level/02_smote.pbs -------------------------------------------------------------------------------- /03_immune_lineages_experiment/minor_level/07_simulate_test_mixtures.pbs: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/03_immune_lineages_experiment/minor_level/07_simulate_test_mixtures.pbs -------------------------------------------------------------------------------- /03_immune_lineages_experiment/minor_level/07_simulate_train_mixtures.pbs: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/03_immune_lineages_experiment/minor_level/07_simulate_train_mixtures.pbs -------------------------------------------------------------------------------- /03_immune_lineages_experiment/minor_level/08_concatenate_test_adata_objects.pbs: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/03_immune_lineages_experiment/minor_level/08_concatenate_test_adata_objects.pbs -------------------------------------------------------------------------------- /03_immune_lineages_experiment/minor_level/08_concatenate_train_adata_objects.pbs: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/03_immune_lineages_experiment/minor_level/08_concatenate_train_adata_objects.pbs -------------------------------------------------------------------------------- /03_immune_lineages_experiment/minor_level/9_1_prepare_method_specific_data.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/03_immune_lineages_experiment/minor_level/9_1_prepare_method_specific_data.ipynb -------------------------------------------------------------------------------- /03_immune_lineages_experiment/minor_level/9_2_run_bisque.pbs: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/03_immune_lineages_experiment/minor_level/9_2_run_bisque.pbs -------------------------------------------------------------------------------- /03_immune_lineages_experiment/minor_level/9_2_run_bprism.pbs: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/03_immune_lineages_experiment/minor_level/9_2_run_bprism.pbs -------------------------------------------------------------------------------- /03_immune_lineages_experiment/minor_level/9_2_run_cbx.pbs: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/03_immune_lineages_experiment/minor_level/9_2_run_cbx.pbs -------------------------------------------------------------------------------- /03_immune_lineages_experiment/minor_level/9_2_run_cpm_1.pbs: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/03_immune_lineages_experiment/minor_level/9_2_run_cpm_1.pbs -------------------------------------------------------------------------------- /03_immune_lineages_experiment/minor_level/9_2_run_cpm_2.pbs: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/03_immune_lineages_experiment/minor_level/9_2_run_cpm_2.pbs -------------------------------------------------------------------------------- /03_immune_lineages_experiment/minor_level/9_2_run_dwls_1.pbs: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/03_immune_lineages_experiment/minor_level/9_2_run_dwls_1.pbs -------------------------------------------------------------------------------- /03_immune_lineages_experiment/minor_level/9_2_run_dwls_2.pbs: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/03_immune_lineages_experiment/minor_level/9_2_run_dwls_2.pbs -------------------------------------------------------------------------------- /03_immune_lineages_experiment/minor_level/9_2_run_dwls_all.pbs: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/03_immune_lineages_experiment/minor_level/9_2_run_dwls_all.pbs -------------------------------------------------------------------------------- /03_immune_lineages_experiment/minor_level/9_2_run_epic.pbs: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/03_immune_lineages_experiment/minor_level/9_2_run_epic.pbs -------------------------------------------------------------------------------- /03_immune_lineages_experiment/minor_level/9_2_run_hspe.pbs: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/03_immune_lineages_experiment/minor_level/9_2_run_hspe.pbs -------------------------------------------------------------------------------- /03_immune_lineages_experiment/minor_level/9_2_run_music.pbs: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/03_immune_lineages_experiment/minor_level/9_2_run_music.pbs -------------------------------------------------------------------------------- /03_immune_lineages_experiment/minor_level/9_2_run_scaden.pbs: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/03_immune_lineages_experiment/minor_level/9_2_run_scaden.pbs -------------------------------------------------------------------------------- /03_immune_lineages_experiment/minor_level/9_3_collate_test_results.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/03_immune_lineages_experiment/minor_level/9_3_collate_test_results.ipynb -------------------------------------------------------------------------------- /03_immune_lineages_experiment/minor_level/data/Whole_miniatlas_meta_minor_immune_lineages.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/03_immune_lineages_experiment/minor_level/data/Whole_miniatlas_meta_minor_immune_lineages.csv -------------------------------------------------------------------------------- /03_immune_lineages_experiment/subset_level/02_generate_metadata.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/03_immune_lineages_experiment/subset_level/02_generate_metadata.ipynb -------------------------------------------------------------------------------- /03_immune_lineages_experiment/subset_level/02_smote.pbs: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/03_immune_lineages_experiment/subset_level/02_smote.pbs -------------------------------------------------------------------------------- /03_immune_lineages_experiment/subset_level/07_simulate_test_mixtures.pbs: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/03_immune_lineages_experiment/subset_level/07_simulate_test_mixtures.pbs -------------------------------------------------------------------------------- /03_immune_lineages_experiment/subset_level/07_simulate_train_mixtures.pbs: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/03_immune_lineages_experiment/subset_level/07_simulate_train_mixtures.pbs -------------------------------------------------------------------------------- /03_immune_lineages_experiment/subset_level/08_concatenate_test_adata_objects.pbs: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/03_immune_lineages_experiment/subset_level/08_concatenate_test_adata_objects.pbs -------------------------------------------------------------------------------- /03_immune_lineages_experiment/subset_level/08_concatenate_train_adata_objects.pbs: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/03_immune_lineages_experiment/subset_level/08_concatenate_train_adata_objects.pbs -------------------------------------------------------------------------------- /03_immune_lineages_experiment/subset_level/9_1_prepare_method_specific_data.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/03_immune_lineages_experiment/subset_level/9_1_prepare_method_specific_data.ipynb -------------------------------------------------------------------------------- /03_immune_lineages_experiment/subset_level/9_2_run_bisque.pbs: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/03_immune_lineages_experiment/subset_level/9_2_run_bisque.pbs -------------------------------------------------------------------------------- /03_immune_lineages_experiment/subset_level/9_2_run_bprism.pbs: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/03_immune_lineages_experiment/subset_level/9_2_run_bprism.pbs -------------------------------------------------------------------------------- /03_immune_lineages_experiment/subset_level/9_2_run_cbx.pbs: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/03_immune_lineages_experiment/subset_level/9_2_run_cbx.pbs -------------------------------------------------------------------------------- /03_immune_lineages_experiment/subset_level/9_2_run_cpm_1.pbs: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/03_immune_lineages_experiment/subset_level/9_2_run_cpm_1.pbs -------------------------------------------------------------------------------- /03_immune_lineages_experiment/subset_level/9_2_run_cpm_2.pbs: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/03_immune_lineages_experiment/subset_level/9_2_run_cpm_2.pbs -------------------------------------------------------------------------------- /03_immune_lineages_experiment/subset_level/9_2_run_dwls_1.pbs: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/03_immune_lineages_experiment/subset_level/9_2_run_dwls_1.pbs -------------------------------------------------------------------------------- /03_immune_lineages_experiment/subset_level/9_2_run_dwls_2.pbs: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/03_immune_lineages_experiment/subset_level/9_2_run_dwls_2.pbs -------------------------------------------------------------------------------- /03_immune_lineages_experiment/subset_level/9_2_run_dwls_all.pbs: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/03_immune_lineages_experiment/subset_level/9_2_run_dwls_all.pbs -------------------------------------------------------------------------------- /03_immune_lineages_experiment/subset_level/9_2_run_epic.pbs: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/03_immune_lineages_experiment/subset_level/9_2_run_epic.pbs -------------------------------------------------------------------------------- /03_immune_lineages_experiment/subset_level/9_2_run_hspe.pbs: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/03_immune_lineages_experiment/subset_level/9_2_run_hspe.pbs -------------------------------------------------------------------------------- /03_immune_lineages_experiment/subset_level/9_2_run_music.pbs: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/03_immune_lineages_experiment/subset_level/9_2_run_music.pbs -------------------------------------------------------------------------------- /03_immune_lineages_experiment/subset_level/9_2_run_scaden.pbs: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/03_immune_lineages_experiment/subset_level/9_2_run_scaden.pbs -------------------------------------------------------------------------------- /03_immune_lineages_experiment/subset_level/9_3_collate_test_results.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/03_immune_lineages_experiment/subset_level/9_3_collate_test_results.ipynb -------------------------------------------------------------------------------- /03_immune_lineages_experiment/subset_level/data/Whole_miniatlas_meta_immune_lineages_remastered.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/03_immune_lineages_experiment/subset_level/data/Whole_miniatlas_meta_immune_lineages_remastered.csv -------------------------------------------------------------------------------- /04_tcga_bulk_validation/0_collect_raw_counts.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/04_tcga_bulk_validation/0_collect_raw_counts.ipynb -------------------------------------------------------------------------------- /04_tcga_bulk_validation/10_validation.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/04_tcga_bulk_validation/10_validation.ipynb -------------------------------------------------------------------------------- /04_tcga_bulk_validation/9_1_prepare_tool_specific_data.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/04_tcga_bulk_validation/9_1_prepare_tool_specific_data.ipynb -------------------------------------------------------------------------------- /04_tcga_bulk_validation/9_2_run_bisque.pbs: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/04_tcga_bulk_validation/9_2_run_bisque.pbs -------------------------------------------------------------------------------- /04_tcga_bulk_validation/9_2_run_bprism.pbs: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/04_tcga_bulk_validation/9_2_run_bprism.pbs -------------------------------------------------------------------------------- /04_tcga_bulk_validation/9_2_run_cbx.pbs: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/04_tcga_bulk_validation/9_2_run_cbx.pbs -------------------------------------------------------------------------------- /04_tcga_bulk_validation/9_2_run_cpm_1.pbs: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/04_tcga_bulk_validation/9_2_run_cpm_1.pbs -------------------------------------------------------------------------------- /04_tcga_bulk_validation/9_2_run_cpm_2.pbs: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/04_tcga_bulk_validation/9_2_run_cpm_2.pbs -------------------------------------------------------------------------------- /04_tcga_bulk_validation/9_2_run_dwls_1.pbs: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/04_tcga_bulk_validation/9_2_run_dwls_1.pbs -------------------------------------------------------------------------------- /04_tcga_bulk_validation/9_2_run_dwls_2.pbs: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/04_tcga_bulk_validation/9_2_run_dwls_2.pbs -------------------------------------------------------------------------------- /04_tcga_bulk_validation/9_2_run_epic.pbs: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/04_tcga_bulk_validation/9_2_run_epic.pbs -------------------------------------------------------------------------------- /04_tcga_bulk_validation/9_2_run_hspe.pbs: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/04_tcga_bulk_validation/9_2_run_hspe.pbs -------------------------------------------------------------------------------- /04_tcga_bulk_validation/9_2_run_music.pbs: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/04_tcga_bulk_validation/9_2_run_music.pbs -------------------------------------------------------------------------------- /04_tcga_bulk_validation/9_2_run_scaden.pbs: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/04_tcga_bulk_validation/9_2_run_scaden.pbs -------------------------------------------------------------------------------- /04_tcga_bulk_validation/9_3_collate_test_results.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/04_tcga_bulk_validation/9_3_collate_test_results.ipynb -------------------------------------------------------------------------------- /04_tcga_bulk_validation/data/Whole_miniatlas_meta_9_10.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/04_tcga_bulk_validation/data/Whole_miniatlas_meta_9_10.csv -------------------------------------------------------------------------------- /05_external_scrna_validation/bassez_et_al/00_cell_counts_analysis.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/05_external_scrna_validation/bassez_et_al/00_cell_counts_analysis.ipynb -------------------------------------------------------------------------------- /05_external_scrna_validation/bassez_et_al/00_consolidate_immune_lineages.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/05_external_scrna_validation/bassez_et_al/00_consolidate_immune_lineages.ipynb -------------------------------------------------------------------------------- /05_external_scrna_validation/bassez_et_al/01_normalize_raw_counts.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/05_external_scrna_validation/bassez_et_al/01_normalize_raw_counts.R -------------------------------------------------------------------------------- /05_external_scrna_validation/bassez_et_al/01_normalize_raw_counts.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/05_external_scrna_validation/bassez_et_al/01_normalize_raw_counts.ipynb -------------------------------------------------------------------------------- /05_external_scrna_validation/bassez_et_al/02_generate_metadata.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/05_external_scrna_validation/bassez_et_al/02_generate_metadata.ipynb -------------------------------------------------------------------------------- /05_external_scrna_validation/bassez_et_al/02_smote.pbs: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/05_external_scrna_validation/bassez_et_al/02_smote.pbs -------------------------------------------------------------------------------- /05_external_scrna_validation/bassez_et_al/04_1_seurat_individual_patient.pbs: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/05_external_scrna_validation/bassez_et_al/04_1_seurat_individual_patient.pbs -------------------------------------------------------------------------------- /05_external_scrna_validation/bassez_et_al/05_investigate_smoted_umap.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/05_external_scrna_validation/bassez_et_al/05_investigate_smoted_umap.ipynb -------------------------------------------------------------------------------- /05_external_scrna_validation/bassez_et_al/07_simulate_test_mixtures.pbs: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/05_external_scrna_validation/bassez_et_al/07_simulate_test_mixtures.pbs -------------------------------------------------------------------------------- /05_external_scrna_validation/bassez_et_al/07_simulate_train_mixtures.pbs: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/05_external_scrna_validation/bassez_et_al/07_simulate_train_mixtures.pbs -------------------------------------------------------------------------------- /05_external_scrna_validation/bassez_et_al/9_1_prepare_tool_specific_data.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/05_external_scrna_validation/bassez_et_al/9_1_prepare_tool_specific_data.ipynb -------------------------------------------------------------------------------- /05_external_scrna_validation/bassez_et_al/9_2_run_bisque.pbs: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/05_external_scrna_validation/bassez_et_al/9_2_run_bisque.pbs -------------------------------------------------------------------------------- /05_external_scrna_validation/bassez_et_al/9_2_run_bprism.pbs: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/05_external_scrna_validation/bassez_et_al/9_2_run_bprism.pbs -------------------------------------------------------------------------------- /05_external_scrna_validation/bassez_et_al/9_2_run_cbx.pbs: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/05_external_scrna_validation/bassez_et_al/9_2_run_cbx.pbs -------------------------------------------------------------------------------- /05_external_scrna_validation/bassez_et_al/9_2_run_dwls_1.pbs: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/05_external_scrna_validation/bassez_et_al/9_2_run_dwls_1.pbs -------------------------------------------------------------------------------- /05_external_scrna_validation/bassez_et_al/9_2_run_dwls_2.pbs: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/05_external_scrna_validation/bassez_et_al/9_2_run_dwls_2.pbs -------------------------------------------------------------------------------- /05_external_scrna_validation/bassez_et_al/9_2_run_epic.pbs: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/05_external_scrna_validation/bassez_et_al/9_2_run_epic.pbs -------------------------------------------------------------------------------- /05_external_scrna_validation/bassez_et_al/9_2_run_hspe.pbs: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/05_external_scrna_validation/bassez_et_al/9_2_run_hspe.pbs -------------------------------------------------------------------------------- /05_external_scrna_validation/bassez_et_al/9_2_run_music.pbs: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/05_external_scrna_validation/bassez_et_al/9_2_run_music.pbs -------------------------------------------------------------------------------- /05_external_scrna_validation/bassez_et_al/9_2_run_scaden.pbs: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/05_external_scrna_validation/bassez_et_al/9_2_run_scaden.pbs -------------------------------------------------------------------------------- /05_external_scrna_validation/bassez_et_al/9_3_collate_test_results.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/05_external_scrna_validation/bassez_et_al/9_3_collate_test_results.ipynb -------------------------------------------------------------------------------- /05_external_scrna_validation/bassez_et_al/data/Miniatlas_meta_9_10.tsv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/05_external_scrna_validation/bassez_et_al/data/Miniatlas_meta_9_10.tsv -------------------------------------------------------------------------------- /05_external_scrna_validation/pal_et_al/00_consolidate_cell_annotations.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/05_external_scrna_validation/pal_et_al/00_consolidate_cell_annotations.ipynb -------------------------------------------------------------------------------- /05_external_scrna_validation/pal_et_al/01_normalize_raw_counts.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/05_external_scrna_validation/pal_et_al/01_normalize_raw_counts.ipynb -------------------------------------------------------------------------------- /05_external_scrna_validation/pal_et_al/02_generate_metadata.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/05_external_scrna_validation/pal_et_al/02_generate_metadata.ipynb -------------------------------------------------------------------------------- /05_external_scrna_validation/pal_et_al/02_smote.pbs: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/05_external_scrna_validation/pal_et_al/02_smote.pbs -------------------------------------------------------------------------------- /05_external_scrna_validation/pal_et_al/04_1_seurat_individual_patient.pbs: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/05_external_scrna_validation/pal_et_al/04_1_seurat_individual_patient.pbs -------------------------------------------------------------------------------- /05_external_scrna_validation/pal_et_al/05_qa_smote_cells.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/05_external_scrna_validation/pal_et_al/05_qa_smote_cells.ipynb -------------------------------------------------------------------------------- /05_external_scrna_validation/pal_et_al/06_filter_smoted_counts.pbs: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/05_external_scrna_validation/pal_et_al/06_filter_smoted_counts.pbs -------------------------------------------------------------------------------- /05_external_scrna_validation/pal_et_al/07_simulate_test_mixtures.pbs: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/05_external_scrna_validation/pal_et_al/07_simulate_test_mixtures.pbs -------------------------------------------------------------------------------- /05_external_scrna_validation/pal_et_al/07_simulate_train_mixtures.pbs: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/05_external_scrna_validation/pal_et_al/07_simulate_train_mixtures.pbs -------------------------------------------------------------------------------- /05_external_scrna_validation/pal_et_al/09_1_prepare_tool_specific_data.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/05_external_scrna_validation/pal_et_al/09_1_prepare_tool_specific_data.ipynb -------------------------------------------------------------------------------- /05_external_scrna_validation/pal_et_al/09_2_run_bisque.pbs: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/05_external_scrna_validation/pal_et_al/09_2_run_bisque.pbs -------------------------------------------------------------------------------- /05_external_scrna_validation/pal_et_al/09_2_run_bprism.pbs: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/05_external_scrna_validation/pal_et_al/09_2_run_bprism.pbs -------------------------------------------------------------------------------- /05_external_scrna_validation/pal_et_al/09_2_run_cbx.pbs: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/05_external_scrna_validation/pal_et_al/09_2_run_cbx.pbs -------------------------------------------------------------------------------- /05_external_scrna_validation/pal_et_al/09_2_run_dwls_1.pbs: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/05_external_scrna_validation/pal_et_al/09_2_run_dwls_1.pbs -------------------------------------------------------------------------------- /05_external_scrna_validation/pal_et_al/09_2_run_dwls_2.pbs: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/05_external_scrna_validation/pal_et_al/09_2_run_dwls_2.pbs -------------------------------------------------------------------------------- /05_external_scrna_validation/pal_et_al/09_2_run_epic.pbs: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/05_external_scrna_validation/pal_et_al/09_2_run_epic.pbs -------------------------------------------------------------------------------- /05_external_scrna_validation/pal_et_al/09_2_run_hspe.pbs: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/05_external_scrna_validation/pal_et_al/09_2_run_hspe.pbs -------------------------------------------------------------------------------- /05_external_scrna_validation/pal_et_al/09_2_run_music.pbs: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/05_external_scrna_validation/pal_et_al/09_2_run_music.pbs -------------------------------------------------------------------------------- /05_external_scrna_validation/pal_et_al/09_2_run_scaden.pbs: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/05_external_scrna_validation/pal_et_al/09_2_run_scaden.pbs -------------------------------------------------------------------------------- /05_external_scrna_validation/pal_et_al/09_3_collate_test_results.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/05_external_scrna_validation/pal_et_al/09_3_collate_test_results.ipynb -------------------------------------------------------------------------------- /05_external_scrna_validation/pal_et_al/data/Miniatlas_meta_major.tsv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/05_external_scrna_validation/pal_et_al/data/Miniatlas_meta_major.tsv -------------------------------------------------------------------------------- /06_batch_effect_validation/bassez_et_al/00_consolidate_immune_lineages.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/06_batch_effect_validation/bassez_et_al/00_consolidate_immune_lineages.ipynb -------------------------------------------------------------------------------- /06_batch_effect_validation/bassez_et_al/02_generate_metadata.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/06_batch_effect_validation/bassez_et_al/02_generate_metadata.ipynb -------------------------------------------------------------------------------- /06_batch_effect_validation/bassez_et_al/02_smote.pbs: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/06_batch_effect_validation/bassez_et_al/02_smote.pbs -------------------------------------------------------------------------------- /06_batch_effect_validation/bassez_et_al/04_1_seurat_individual_patient.pbs: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/06_batch_effect_validation/bassez_et_al/04_1_seurat_individual_patient.pbs -------------------------------------------------------------------------------- /06_batch_effect_validation/bassez_et_al/05_investigate_smoted_umap.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/06_batch_effect_validation/bassez_et_al/05_investigate_smoted_umap.ipynb -------------------------------------------------------------------------------- /06_batch_effect_validation/bassez_et_al/07_simulate_test_mixtures.pbs: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/06_batch_effect_validation/bassez_et_al/07_simulate_test_mixtures.pbs -------------------------------------------------------------------------------- /06_batch_effect_validation/bassez_et_al/09_1_prepare_tool_specific_data.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/06_batch_effect_validation/bassez_et_al/09_1_prepare_tool_specific_data.ipynb -------------------------------------------------------------------------------- /06_batch_effect_validation/bassez_et_al/09_2_run_bisque.pbs: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/06_batch_effect_validation/bassez_et_al/09_2_run_bisque.pbs -------------------------------------------------------------------------------- /06_batch_effect_validation/bassez_et_al/09_2_run_bprism_v2.pbs: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/06_batch_effect_validation/bassez_et_al/09_2_run_bprism_v2.pbs -------------------------------------------------------------------------------- /06_batch_effect_validation/bassez_et_al/09_2_run_cbx.pbs: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/06_batch_effect_validation/bassez_et_al/09_2_run_cbx.pbs -------------------------------------------------------------------------------- /06_batch_effect_validation/bassez_et_al/09_2_run_dwls_1.pbs: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/06_batch_effect_validation/bassez_et_al/09_2_run_dwls_1.pbs -------------------------------------------------------------------------------- /06_batch_effect_validation/bassez_et_al/09_2_run_dwls_2.pbs: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/06_batch_effect_validation/bassez_et_al/09_2_run_dwls_2.pbs -------------------------------------------------------------------------------- /06_batch_effect_validation/bassez_et_al/09_2_run_epic.pbs: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/06_batch_effect_validation/bassez_et_al/09_2_run_epic.pbs -------------------------------------------------------------------------------- /06_batch_effect_validation/bassez_et_al/09_2_run_hspe.pbs: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/06_batch_effect_validation/bassez_et_al/09_2_run_hspe.pbs -------------------------------------------------------------------------------- /06_batch_effect_validation/bassez_et_al/09_2_run_music.pbs: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/06_batch_effect_validation/bassez_et_al/09_2_run_music.pbs -------------------------------------------------------------------------------- /06_batch_effect_validation/bassez_et_al/09_2_run_scaden.pbs: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/06_batch_effect_validation/bassez_et_al/09_2_run_scaden.pbs -------------------------------------------------------------------------------- /06_batch_effect_validation/bassez_et_al/09_3_collate_test_results.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/06_batch_effect_validation/bassez_et_al/09_3_collate_test_results.ipynb -------------------------------------------------------------------------------- /06_batch_effect_validation/bassez_et_al/data/Miniatlas_major_immune_lineage.tsv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/06_batch_effect_validation/bassez_et_al/data/Miniatlas_major_immune_lineage.tsv -------------------------------------------------------------------------------- /06_batch_effect_validation/pal_et_al/00_consolidate_cell_annotations.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/06_batch_effect_validation/pal_et_al/00_consolidate_cell_annotations.ipynb -------------------------------------------------------------------------------- /06_batch_effect_validation/pal_et_al/02_generate_metadata.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/06_batch_effect_validation/pal_et_al/02_generate_metadata.ipynb -------------------------------------------------------------------------------- /06_batch_effect_validation/pal_et_al/02_smote.pbs: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/06_batch_effect_validation/pal_et_al/02_smote.pbs -------------------------------------------------------------------------------- /06_batch_effect_validation/pal_et_al/04_1_seurat_individual_patient.pbs: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/06_batch_effect_validation/pal_et_al/04_1_seurat_individual_patient.pbs -------------------------------------------------------------------------------- /06_batch_effect_validation/pal_et_al/07_simulate_test_mixtures.pbs: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/06_batch_effect_validation/pal_et_al/07_simulate_test_mixtures.pbs -------------------------------------------------------------------------------- /06_batch_effect_validation/pal_et_al/09_1_prepare_tool_specific_data.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/06_batch_effect_validation/pal_et_al/09_1_prepare_tool_specific_data.ipynb -------------------------------------------------------------------------------- /06_batch_effect_validation/pal_et_al/09_2_run_bisque.pbs: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/06_batch_effect_validation/pal_et_al/09_2_run_bisque.pbs -------------------------------------------------------------------------------- /06_batch_effect_validation/pal_et_al/09_2_run_bprism_v2.pbs: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/06_batch_effect_validation/pal_et_al/09_2_run_bprism_v2.pbs -------------------------------------------------------------------------------- /06_batch_effect_validation/pal_et_al/09_2_run_cbx.pbs: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/06_batch_effect_validation/pal_et_al/09_2_run_cbx.pbs -------------------------------------------------------------------------------- /06_batch_effect_validation/pal_et_al/09_2_run_dwls_1.pbs: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/06_batch_effect_validation/pal_et_al/09_2_run_dwls_1.pbs -------------------------------------------------------------------------------- /06_batch_effect_validation/pal_et_al/09_2_run_dwls_2.pbs: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/06_batch_effect_validation/pal_et_al/09_2_run_dwls_2.pbs -------------------------------------------------------------------------------- /06_batch_effect_validation/pal_et_al/09_2_run_epic.pbs: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/06_batch_effect_validation/pal_et_al/09_2_run_epic.pbs -------------------------------------------------------------------------------- /06_batch_effect_validation/pal_et_al/09_2_run_hspe.pbs: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/06_batch_effect_validation/pal_et_al/09_2_run_hspe.pbs -------------------------------------------------------------------------------- /06_batch_effect_validation/pal_et_al/09_2_run_music.pbs: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/06_batch_effect_validation/pal_et_al/09_2_run_music.pbs -------------------------------------------------------------------------------- /06_batch_effect_validation/pal_et_al/09_2_run_scaden.pbs: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/06_batch_effect_validation/pal_et_al/09_2_run_scaden.pbs -------------------------------------------------------------------------------- /06_batch_effect_validation/pal_et_al/09_3_collate_test_results.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/06_batch_effect_validation/pal_et_al/09_3_collate_test_results.ipynb -------------------------------------------------------------------------------- /06_batch_effect_validation/pal_et_al/data/Miniatlas_major_immune_lineage.tsv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/06_batch_effect_validation/pal_et_al/data/Miniatlas_major_immune_lineage.tsv -------------------------------------------------------------------------------- /CITATION.cff: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/CITATION.cff -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/LICENSE -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/README.md -------------------------------------------------------------------------------- /params/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/params/README.md -------------------------------------------------------------------------------- /params/sample_input_file.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/params/sample_input_file.csv -------------------------------------------------------------------------------- /params/seurat_CCA_params_file.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/params/seurat_CCA_params_file.csv -------------------------------------------------------------------------------- /params/seurat_gene_input_file.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/params/seurat_gene_input_file.csv -------------------------------------------------------------------------------- /params/seurat_params_file.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/params/seurat_params_file.csv -------------------------------------------------------------------------------- /src/02_smote.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/src/02_smote.py -------------------------------------------------------------------------------- /src/03_transpose_smoted_data.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/src/03_transpose_smoted_data.py -------------------------------------------------------------------------------- /src/04_1_seurat_individual_patient.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/src/04_1_seurat_individual_patient.R -------------------------------------------------------------------------------- /src/04_2_seurat_integration.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/src/04_2_seurat_integration.R -------------------------------------------------------------------------------- /src/06_filter_smoted_counts.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/src/06_filter_smoted_counts.py -------------------------------------------------------------------------------- /src/07_simulate_test_mixtures.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/src/07_simulate_test_mixtures.py -------------------------------------------------------------------------------- /src/07_simulate_train_menden_et_al_method.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/src/07_simulate_train_menden_et_al_method.py -------------------------------------------------------------------------------- /src/07_simulate_train_mixtures_sparse_method.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/src/07_simulate_train_mixtures_sparse_method.py -------------------------------------------------------------------------------- /src/08_concatenate_test_adata_objects.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/src/08_concatenate_test_adata_objects.py -------------------------------------------------------------------------------- /src/08_concatenate_train_adata_objects.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/src/08_concatenate_train_adata_objects.py -------------------------------------------------------------------------------- /src/9_2_run_bisque.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/src/9_2_run_bisque.R -------------------------------------------------------------------------------- /src/9_2_run_bprism.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/src/9_2_run_bprism.R -------------------------------------------------------------------------------- /src/9_2_run_cpm.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/src/9_2_run_cpm.R -------------------------------------------------------------------------------- /src/9_2_run_cpm_1.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/src/9_2_run_cpm_1.R -------------------------------------------------------------------------------- /src/9_2_run_cpm_2.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/src/9_2_run_cpm_2.R -------------------------------------------------------------------------------- /src/9_2_run_dwls_1.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/src/9_2_run_dwls_1.R -------------------------------------------------------------------------------- /src/9_2_run_dwls_2.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/src/9_2_run_dwls_2.R -------------------------------------------------------------------------------- /src/9_2_run_dwls_all.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/src/9_2_run_dwls_all.R -------------------------------------------------------------------------------- /src/9_2_run_epic.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/src/9_2_run_epic.R -------------------------------------------------------------------------------- /src/9_2_run_hspe.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/src/9_2_run_hspe.R -------------------------------------------------------------------------------- /src/9_2_run_music.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/src/9_2_run_music.R -------------------------------------------------------------------------------- /src/utils/1_CPM_functions.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/src/utils/1_CPM_functions.R -------------------------------------------------------------------------------- /src/utils/1_DWLS_de_analysis.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/src/utils/1_DWLS_de_analysis.R -------------------------------------------------------------------------------- /src/utils/1_DWLS_deconvolution.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/src/utils/1_DWLS_deconvolution.R -------------------------------------------------------------------------------- /src/utils/1_DWLS_functions.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/src/utils/1_DWLS_functions.R -------------------------------------------------------------------------------- /visualizations/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/visualizations/README.md -------------------------------------------------------------------------------- /visualizations/main_fig_2_a_b.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/visualizations/main_fig_2_a_b.ipynb -------------------------------------------------------------------------------- /visualizations/main_fig_2_c_d.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/visualizations/main_fig_2_c_d.ipynb -------------------------------------------------------------------------------- /visualizations/main_fig_3.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/visualizations/main_fig_3.ipynb -------------------------------------------------------------------------------- /visualizations/main_fig_4a.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/visualizations/main_fig_4a.ipynb -------------------------------------------------------------------------------- /visualizations/main_fig_4b_c.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/visualizations/main_fig_4b_c.ipynb -------------------------------------------------------------------------------- /visualizations/main_fig_5_b_c.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/visualizations/main_fig_5_b_c.ipynb -------------------------------------------------------------------------------- /visualizations/main_fig_5a_d_e.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/visualizations/main_fig_5a_d_e.ipynb -------------------------------------------------------------------------------- /visualizations/supplementary_fig_10a_b.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/visualizations/supplementary_fig_10a_b.ipynb -------------------------------------------------------------------------------- /visualizations/supplementary_fig_10c_d.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/visualizations/supplementary_fig_10c_d.ipynb -------------------------------------------------------------------------------- /visualizations/supplementary_fig_12.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/visualizations/supplementary_fig_12.ipynb -------------------------------------------------------------------------------- /visualizations/supplementary_fig_13.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/visualizations/supplementary_fig_13.ipynb -------------------------------------------------------------------------------- /visualizations/supplementary_fig_14.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/visualizations/supplementary_fig_14.ipynb -------------------------------------------------------------------------------- /visualizations/supplementary_fig_15.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/visualizations/supplementary_fig_15.ipynb -------------------------------------------------------------------------------- /visualizations/supplementary_fig_16.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/visualizations/supplementary_fig_16.ipynb -------------------------------------------------------------------------------- /visualizations/supplementary_fig_17a_b.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/visualizations/supplementary_fig_17a_b.ipynb -------------------------------------------------------------------------------- /visualizations/supplementary_fig_17c_d.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/visualizations/supplementary_fig_17c_d.ipynb -------------------------------------------------------------------------------- /visualizations/supplementary_fig_17e_f.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/visualizations/supplementary_fig_17e_f.ipynb -------------------------------------------------------------------------------- /visualizations/supplementary_fig_18.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/visualizations/supplementary_fig_18.ipynb -------------------------------------------------------------------------------- /visualizations/supplementary_fig_1a_c_e.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/visualizations/supplementary_fig_1a_c_e.ipynb -------------------------------------------------------------------------------- /visualizations/supplementary_fig_1b_d_f.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/visualizations/supplementary_fig_1b_d_f.ipynb -------------------------------------------------------------------------------- /visualizations/supplementary_fig_2.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/visualizations/supplementary_fig_2.ipynb -------------------------------------------------------------------------------- /visualizations/supplementary_fig_3.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/visualizations/supplementary_fig_3.ipynb -------------------------------------------------------------------------------- /visualizations/supplementary_fig_4_11.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/visualizations/supplementary_fig_4_11.ipynb -------------------------------------------------------------------------------- /visualizations/supplementary_fig_5.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/visualizations/supplementary_fig_5.ipynb -------------------------------------------------------------------------------- /visualizations/supplementary_fig_6.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/visualizations/supplementary_fig_6.ipynb -------------------------------------------------------------------------------- /visualizations/supplementary_fig_7a_b_8a.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/visualizations/supplementary_fig_7a_b_8a.ipynb -------------------------------------------------------------------------------- /visualizations/supplementary_fig_7c_d_8b.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/visualizations/supplementary_fig_7c_d_8b.ipynb -------------------------------------------------------------------------------- /visualizations/supplementary_fig_9.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MedicalGenomicsLab/deconvolution_benchmarking/HEAD/visualizations/supplementary_fig_9.ipynb --------------------------------------------------------------------------------