├── .Rhistory ├── .gitattributes ├── README.md ├── input_tables ├── DE_LCAMhi_vs_LCAMlo_pseudobulk.rd ├── GSE127465_human_cell_metadata_54773x25.tsv.gz ├── TCGA-LUAD_clinical.csv ├── TCGA_ESTIMATE.txt ├── TCGA_abbreviations.csv ├── Thorsson_et_al_TCGA_tumor_immunology_metrics.csv ├── annots_list.csv ├── cell_metadata.csv ├── chakarov_Table_S4.csv ├── chakarov_Table_S5.csv ├── cluster_order_list.txt ├── ensemble_ids.tsv ├── immune_vs_ep_de.csv ├── lig_rec_lcamhi_vs_lcamlo.rd ├── lig_rec_lcamhi_vs_normal.rd ├── lig_rec_lcamlo_vs_normal.rd ├── ligand_receptor_ramilowski2015.csv ├── mSignatureDB_profiles.txt ├── markers_in_figures.csv ├── table_s1_sample_table.csv ├── table_s5_genes_used_in_figures.csv └── table_s5_signature_scores.csv └── scripts ├── .Rhistory ├── figure_1cde.R ├── figure_1f.r ├── figure_1g.R ├── figure_2ab.R ├── figure_2c_s2c.R ├── figure_2dh_s2j.R ├── figure_2g_s2de.R ├── figure_3a.R ├── figure_3b.R ├── figure_3c_s3efgh.R ├── figure_3def_s3i.R ├── figure_3g.R ├── figure_3h.R ├── figure_4ab.r ├── figure_4c_s4l.R ├── figure_4de_s4ijk.R ├── figure_4fg.R ├── figure_5abcd_s5a.R ├── figure_5hijklm_s5jk.R ├── figure_6ac_s6abcdefjklmnopqr_7abcd_s7ab.R ├── figure_6b_s6ghi.R ├── figure_7ef_s7cd.R ├── figure_s1bc.R ├── figure_s1de.R ├── figure_s1g.R ├── figure_s1hi.R ├── figure_s2ab.R ├── figure_s2fghi.R ├── figure_s3a.R ├── figure_s3b.R ├── figure_s4abce.R ├── figure_s4d.R ├── figure_s4fgh.R ├── figures_main.R ├── get_LCAM_scores.R ├── normalize_adt_data.R ├── run_clustering.R ├── scClustering ├── DE.r ├── clustering3.r ├── make_LSF_EM_job_file.r ├── make_LSF_seeding_job_file.r ├── run_EM.r ├── run_get_seed.r └── umitab_utils.r └── tcr_output_to_analysis.R /.Rhistory: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/effiken/Leader_et_al/HEAD/.Rhistory -------------------------------------------------------------------------------- /.gitattributes: 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