SpaCon_results_reproduction documentation

This tutorial contains detailed reproduction code for the main results in the article “SpaCon: Integrative Analysis of Spatial Transcriptome and Connectome”.

The processed data can be downloaded from https://drive.google.com/drive/folders/1lQQQVjXt8lvciuKq_Jkp4LGsR_EQXFAi?usp=sharing

Contents:

• 1_ctx_th_connection_and_gene_exp_cluster
  • ctx to th connection cluster
  • gene exp umap
• 2_ctx_th_connection_and_th_gene_pc1
  • scanpy
• 3_ctx_th_connection_and_gene_correlation
  • subregion th ctx correlation
• 4_ctx_layer56_and_th_correlation
  • ctx layer56 th correlation
• 5_ctx_th_gene_analysis
  • ctx layer56 th correlation
• 6_ctx_cc_intracellular_extracellular_compare
  • gene exp plot
  • ctx layer maker gene in cc
• 7_cc_mRNA_and_cell_plot
  • plot
  • cell seg plot
• 8_coronal_sagittal_cc_in_out_deg_compare
• 9_ctx_3region_DEGs_expression_in_cc
  • gene exp data
• 10_ctx_cc_connection_and_correlation
  • conn data
  • gene exp data
• 11_PLS_find_metagene
  • PLS