Differentially expressed genes (DEGs) for Cognitive Resilience (CR) and Cognitive Decline Resilience (CDR)

The folders with the "_CR_score" tag are DEGs computed against the cognitive resilience score (CR score). This is calculated using the AD pathology measurement (gpath, nft, plaq_n, tangles) and global cognition at last visit (cogn_global_lv).
gpath_CR_score/
nft_CR_score/
plaq_n_CR_score/
tangles_CR_score/

The folders with the "_CDR_score" tag are DEGs computed against the cognitive decline resilience score (CDR score). This is calculated using the AD pathology measurement (gpath, nft, plaq_n, tangles) and the rate of decline of global cognition (cogng_random_slope).
gpath_CDR_score/
nft_CDR_score/
plaq_n_CDR_score/
tangles_CDR_score/

The folder with cogdx AD is for DEGs computed between pathologic diagnosis of AD using NIA-Reagan scores (as described in the methods) against cognitive diagnosis of AD.
cogdx_AD_yes/

The folders with the "_corrected" tag are DEGs computed by adding the AD pathology measurement (gpath, nft, plaq_n, tangles) as a covariate instead of using the CR or CDR score. This is described in the methods of the paper. Subfolders separate the results into those for cogn_global_lv (global cognition) and cogng_random_slope (rate of decline of global cognition).
cognition_gpath_corrected/
cognition_nft_corrected/
cognition_plaq_n_corrected/
cognition_tangles_corrected/

DEG csv files have the following columns:
gene - HGNC symbol
cluster_id - cell type subcluster 
logFC, logCPM, F, p_val - from Muscat
p_adj.loc - locally adjusted p-values (on each cell type separately)
p_adj.glb - globally adjusted p-values