The directories "expression" and "expression_nonlog" process scRNA-seq data according to cell type and stage at log2 and nonlog2 scale, respectively.

The directory "gene_set" contains NDD gene sets and performs overlap analysis.

Code in these three directories should be run before co-expression enrichment, expression change, and other analyses.

Code in these three directories can be run as follows:

setwd("./expression/")

source("process_data.R")

source("divide_cell_type.R")

source("divide_cell_subcluster.R")

source("divide_NPC_subtype.R")

source("NPC_transition.R")

source("NPC_Ex_differentiation.R")

source("NPC subtype_Ex_differentiation.R")

source("calculate_size.R")

setwd("../expression_nonlog/")

source("divide_cell_type.R")

source("divide_NPC_subtype.R")

source("calculate_FC.R")

setwd("../expression/")

source("calculate_bin.R")

setwd("../gene_set/")

source("calculate_size.R")

source("calculate_size_1.R")

source("calculate_size_CADD.R")

source("calculate_overlap.R")

source("plot_overlap.R")


The directories "coexpression", "coexpression_stage", and "coexpression_transition" perform co-expression enrichment analysis of NDD genes in six major cell types, cell stages, and cell transitions, respectively.

The directories "coexpression_NPC_Ex", "coexpression_vRG_Ex", "coexpression_oRG_Ex", and "coexpression_IPC_Ex" perform co-expression enrichment analysis of NDD genes during differentiation from NPCs and NPC subtypes to excitatory neurons.


The directory "expression_NPC" performs expression change analysis of NDD genes during transitions within NPC subtypes.

The directories "expression_NPC_Ex", "expression_vRG_Ex", "expression_oRG_Ex", and "expression_IPC_Ex" perform expression change analysis of NDD genes during differentiation from NPCs and NPC subtypes to excitatory neurons.


The directory "GO_overlap" performs GO enrichment analysis of dnLoF-ASD and dnMis-Epi genes during the vRG-to-IPC transition at GW10.

The directories "GO_positive_correlation" and "GO_negative_correlation" perform GO correlation analysis of dnLoF-ASD and dnMis-Epi genes during the vRG-to-IPC transition at GW10.

The directories "GO_expression_increase" and "GO_expression_decrease" perform GO expression change analysis during the vRG-to-IPC transition at GW10.


The directory "CHD8" performs CHD8 target gene analysis.


The directory "network_cell_type" performs coexpression network analysis of dnLoF-ASD and dnMis-Epi genes in six major cell types.

The directory "network_transition" performs coexpression network analysis of dnLoF-ASD and dnMis-Epi genes during the vRG-to-IPC transition at GW10.

The directory "network_NI" performs coexpression network analysis of ASD genes with dnLoF mutations in NPCs, and epilepsy genes with dnMis mutations in interneurons.


Please see the file "README.txt" in each directory for more details.
