├── README.md └── code ├── .DS_Store ├── .Rhistory ├── Calculating_HNSCC_and_MCF10A_EMT_epithelial_signature_scores.R ├── Calculating_HuMEC_MCF10A_EMT_epithelial_signature_scores.R ├── Deficiencies_in_TGFβ_induced_EMT_in_CROPseq_perturbed_MCF10A_cells.R ├── Determining_enrichment_of_CROPseq_pertubed_MCF10A_cells_across_pseudospace.R ├── Dynamic_time_warping_alignment_of_MCF10A_pseudospatial_trajectories.R ├── GSA_hyper_helper_functions.R ├── Generating_Puram_et_al_HNSCC_cds_object.R ├── HNSCC_and_MCF10A_EMT_and_epithelal_signature_scores_&_expression_of_putative_EMT_checkpoint_genes.R ├── Human_GO_bp_no_GO_iea_symbol.gmt ├── KNN_projection_of_HNSCC_and_MCF10A_trajectories.R ├── Pseudospace_support_functions.R ├── Pseudospatial_reconstruction_of_spontaneous_and_TGFB_EMT_in_MCF10A_cells.R ├── Pseudospatial_reconstruction_of_spontnaeous_and_TGFB_EMT_in_HuMEC_cells.R ├── Trajectory_reconstruction_of_HNSCC_tumor_cells.R ├── c6.all.v6.0.OncogenicSignatures.symbols.gmt ├── 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