BMI_Thesis

A collection of code related to my thesis work

DZ_Annotated.R - code needed to replicate scRNAseq analysis of De Zuani et al, 2024, Nat Comm.

Name		Name	Last commit message	Last commit date
Build_CIBERSORTx_Reference_Final.R		Build_CIBERSORTx_Reference_Final.R
Build_Cell2Location_Reference_Final.R		Build_Cell2Location_Reference_Final.R
DZ_Script_0_HLCA_Centroids_Final.R		DZ_Script_0_HLCA_Centroids_Final.R
DZ_Script_1_Preprocess_Samples_Final.R		DZ_Script_1_Preprocess_Samples_Final.R
DZ_Script_2_Cohort_Integration_Final.R		DZ_Script_2_Cohort_Integration_Final.R
DZ_Script_3_CellChat_Final.R		DZ_Script_3_CellChat_Final.R
DZ_Script_4_CellChat_Analysis_Visualization_Final.R		DZ_Script_4_CellChat_Analysis_Visualization_Final.R
DZ_Script_5_Stats_DEG_Pathway_Final.R		DZ_Script_5_Stats_DEG_Pathway_Final.R
DZ_Script_6_Monocle3_TAM_pseudotime_final.R		DZ_Script_6_Monocle3_TAM_pseudotime_final.R
DZ_Script_7_Pan_Context_UMAP_Counts_Final.R		DZ_Script_7_Pan_Context_UMAP_Counts_Final.R
DZ_Script_8_Companion_Figures_Final.R		DZ_Script_8_Companion_Figures_Final.R
README.md		README.md
TCGA_LUAD_Survival_TAM_Signatures_Final.R		TCGA_LUAD_Survival_TAM_Signatures_Final.R
cell2location_full_pipeline_cleared.ipynb		cell2location_full_pipeline_cleared.ipynb

Navigation Menu