This repository contains the analysis scripts for the human cortical gene program study. The analyses use single nucleus and spatial transcriptomic data from human, macaque and mouse cortex to define human gene programs, examine their cellular and tissue organization, compare their molecular and spatial patterns across species, and relate selected programs to external disease, aging and functional data.
00_setup_and_inputs: source data preparation.01_human_program_derivation_rank_annotation: human program derivation, rank assessment and annotation.02_cellular_preferences_and_regional_effects: cellular preferences and regional effects.03_human_spatial_projection_and_layers: human spatial projection and laminar organization.04_local_subclass_program_relationships: local relationships between cortical subclasses and programs.05_program_program_spatial_associations: local relationships among programs.06_cross_species_nuclear_projection: projection into macaque and mouse nuclei.07_cross_species_spatial_laminar_areal: cross species spatial, laminar and areal comparisons.08_external_annotations: disease, aging and functional annotations.
The scripts are organized by Methods stage. Fig1A.png summarizes the study design.
GO Biological Process enrichment uses each program's saved ranked genes and frozen GMT file. Report aggregation rebuilds the enrichment fields, while program naming and curated term choices remain in downstream naming steps.