├── .gitignore ├── .gitmodules ├── .travis.yml ├── LICENSE ├── README.md ├── Snakefile ├── envs └── bookdown.yml ├── img ├── .gitignore ├── screenshot_mapping.png ├── tcga_correlation_clustered_highlighted.pdf └── tcga_correlation_clustered_highlighted.png ├── lib ├── CIBERSORT │ └── .gitignore ├── dt_caption.R ├── get_slope.R ├── ggthemes.R ├── make_cell_fraction_vector.R └── make_cor.R ├── notebooks ├── 05_input_data.Rmd ├── 10_methods_validity.Rmd ├── 15_mixing_study.Rmd ├── 20_validation_study.Rmd ├── 30_sensitivity_analysis.Rmd ├── 35_spillover_analysis.Rmd ├── 36_spillover_marker_genes.Rmd ├── 70_pub_figures.Rmd ├── 99_bibliography.Rmd ├── _bookdown.yml ├── _impact_of_preprocessing.Rmd ├── _marker_genes_background.Rmd ├── _mrna_bias.Rmd ├── _output.yml ├── _preprocess_single_cell_schelker.Rmd ├── _pres_plots.Rmd ├── _single_cell_marker_genes_nk.Rmd ├── _tcga_comparison.Rmd ├── bibliography.bib ├── config.R └── index.Rmd └── tables ├── color_scales.xlsx ├── fantom5_pdata.xlsx ├── 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