├── 3CA_v2 ├── MP_analysis_new_batch.R ├── README.md ├── cc_analysis.R ├── cc_analysis_consensus_comparison.R ├── ct_specificity.R ├── gene_analysis.R ├── mp_new.R └── pseudobulks.R ├── ITH_hallmarks ├── Generating_MPs │ ├── Generate_Meta_Programs.R │ ├── Genes_nmf_w_basis_example.RDS │ ├── custom_magma.R │ └── robust_nmf_programs.R ├── MPs_distribution │ ├── MP_distribution.R │ ├── MP_list.RDS.gz │ ├── My_study.RDS.gz │ └── heatCols.RDS.gz ├── README.md └── TCGA_analysis │ ├── functions.R │ ├── pdac_classical_main.R │ ├── preprocess_clinical_data.R │ ├── preprocess_mutations.R │ ├── preprocess_tcga_data.R │ ├── study_contribution_per_MP.RDS │ ├── study_tcga_map.R │ ├── tcga_clinical.R │ ├── tcga_clinical_deconv.R │ ├── tcga_clinical_meta.R │ ├── tcga_mp_scores.R │ ├── tcga_mp_scores_deconv.R │ ├── tcga_mutations_new.R │ └── tcga_subtypes_data.R ├── LICENSE ├── README.md ├── aliases_pubmed.R ├── aliases_table.R ├── bins.R ├── canonical_markers.R ├── cc_sigs_consensus.R ├── cna_mat_prep.R ├── functions.R ├── gene_ave.R ├── gene_mp_cor.R ├── gene_mp_cor_all_web.R ├── gene_plots_cell_types.R ├── gene_plots_data_all_web.R ├── gene_plots_render_web.R ├── gene_plots_rmd_web.R ├── mp_scores_all.R ├── mp_scores_prep.R ├── study_plots_cc.R ├── study_plots_cna.R ├── study_plots_ct_comp.R ├── study_plots_ct_umap.R ├── study_plots_data_cc.R ├── study_plots_data_cc_consensus.R ├── study_plots_data_cc_thresh.R ├── study_plots_data_cc_thresh_consensus.R ├── study_plots_data_cna.R ├── study_plots_data_ct_comp.R ├── study_plots_data_ct_umap.R ├── study_plots_data_dist.R └── study_plots_dist.R /3CA_v2/MP_analysis_new_batch.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tiroshlab/3ca/HEAD/3CA_v2/MP_analysis_new_batch.R -------------------------------------------------------------------------------- /3CA_v2/README.md: -------------------------------------------------------------------------------- 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