├── 01.1_Count_matrix_trans.R ├── 01.2_QC_each_matrix.R ├── 01.3_Merge_matrix.R ├── 01.3_Scrublet.py ├── 02_All_cell_clustering.R ├── 03.1_Tumor_copykat_analysis.R ├── 03.2_Cancer_NK_CellphoneDB.R ├── 03_Tumor_cell_analysis_new.R ├── 05.1_T_scvelo.py ├── 05_T_analysis_new.R ├── 06.1_PMo_Cancer_CellphoneDB.R ├── 06.2_DC_Cancer_CellphoneDB.R ├── 06_MF_analysis_new.R ├── 07.1_B_Nichenet.R ├── 07.2_B4_Tfh_CD8_CellphoneDB.R ├── 07_B_analysis_new.R ├── 08.1_N_Nichenet.R ├── 08.2_Neutrophil_SCENIC.R ├── 08.3_Neu_CCL3_Macro_SPP1_CellphoneDB.R ├── 08_Neutrophil_analysis_new.R ├── Cal_fraction.R ├── Cal_fraction_patients.R ├── GSVA.R ├── Heat_Dot_data.R ├── Monocle_plot_gene.R ├── README.md └── my_plot_pseudotime_heatmap.R /01.1_Count_matrix_trans.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Junjie-Hu/NSCLC-immunotherapy/HEAD/01.1_Count_matrix_trans.R -------------------------------------------------------------------------------- /01.2_QC_each_matrix.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Junjie-Hu/NSCLC-immunotherapy/HEAD/01.2_QC_each_matrix.R -------------------------------------------------------------------------------- /01.3_Merge_matrix.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Junjie-Hu/NSCLC-immunotherapy/HEAD/01.3_Merge_matrix.R -------------------------------------------------------------------------------- /01.3_Scrublet.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Junjie-Hu/NSCLC-immunotherapy/HEAD/01.3_Scrublet.py -------------------------------------------------------------------------------- /02_All_cell_clustering.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Junjie-Hu/NSCLC-immunotherapy/HEAD/02_All_cell_clustering.R -------------------------------------------------------------------------------- /03.1_Tumor_copykat_analysis.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Junjie-Hu/NSCLC-immunotherapy/HEAD/03.1_Tumor_copykat_analysis.R -------------------------------------------------------------------------------- /03.2_Cancer_NK_CellphoneDB.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Junjie-Hu/NSCLC-immunotherapy/HEAD/03.2_Cancer_NK_CellphoneDB.R -------------------------------------------------------------------------------- /03_Tumor_cell_analysis_new.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Junjie-Hu/NSCLC-immunotherapy/HEAD/03_Tumor_cell_analysis_new.R -------------------------------------------------------------------------------- /05.1_T_scvelo.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Junjie-Hu/NSCLC-immunotherapy/HEAD/05.1_T_scvelo.py -------------------------------------------------------------------------------- /05_T_analysis_new.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Junjie-Hu/NSCLC-immunotherapy/HEAD/05_T_analysis_new.R -------------------------------------------------------------------------------- /06.1_PMo_Cancer_CellphoneDB.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Junjie-Hu/NSCLC-immunotherapy/HEAD/06.1_PMo_Cancer_CellphoneDB.R -------------------------------------------------------------------------------- /06.2_DC_Cancer_CellphoneDB.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Junjie-Hu/NSCLC-immunotherapy/HEAD/06.2_DC_Cancer_CellphoneDB.R -------------------------------------------------------------------------------- /06_MF_analysis_new.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Junjie-Hu/NSCLC-immunotherapy/HEAD/06_MF_analysis_new.R -------------------------------------------------------------------------------- /07.1_B_Nichenet.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Junjie-Hu/NSCLC-immunotherapy/HEAD/07.1_B_Nichenet.R -------------------------------------------------------------------------------- /07.2_B4_Tfh_CD8_CellphoneDB.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Junjie-Hu/NSCLC-immunotherapy/HEAD/07.2_B4_Tfh_CD8_CellphoneDB.R -------------------------------------------------------------------------------- /07_B_analysis_new.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Junjie-Hu/NSCLC-immunotherapy/HEAD/07_B_analysis_new.R -------------------------------------------------------------------------------- /08.1_N_Nichenet.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Junjie-Hu/NSCLC-immunotherapy/HEAD/08.1_N_Nichenet.R -------------------------------------------------------------------------------- /08.2_Neutrophil_SCENIC.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Junjie-Hu/NSCLC-immunotherapy/HEAD/08.2_Neutrophil_SCENIC.R -------------------------------------------------------------------------------- /08.3_Neu_CCL3_Macro_SPP1_CellphoneDB.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Junjie-Hu/NSCLC-immunotherapy/HEAD/08.3_Neu_CCL3_Macro_SPP1_CellphoneDB.R -------------------------------------------------------------------------------- /08_Neutrophil_analysis_new.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Junjie-Hu/NSCLC-immunotherapy/HEAD/08_Neutrophil_analysis_new.R -------------------------------------------------------------------------------- /Cal_fraction.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Junjie-Hu/NSCLC-immunotherapy/HEAD/Cal_fraction.R -------------------------------------------------------------------------------- /Cal_fraction_patients.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Junjie-Hu/NSCLC-immunotherapy/HEAD/Cal_fraction_patients.R -------------------------------------------------------------------------------- /GSVA.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Junjie-Hu/NSCLC-immunotherapy/HEAD/GSVA.R -------------------------------------------------------------------------------- /Heat_Dot_data.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Junjie-Hu/NSCLC-immunotherapy/HEAD/Heat_Dot_data.R -------------------------------------------------------------------------------- /Monocle_plot_gene.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Junjie-Hu/NSCLC-immunotherapy/HEAD/Monocle_plot_gene.R -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Junjie-Hu/NSCLC-immunotherapy/HEAD/README.md -------------------------------------------------------------------------------- /my_plot_pseudotime_heatmap.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Junjie-Hu/NSCLC-immunotherapy/HEAD/my_plot_pseudotime_heatmap.R --------------------------------------------------------------------------------