Code in this directory can be run as follows:

## Co-expression enrichment analysis of dnLoF-ASD and dnMis-Epi genes during NPC transition at GW10.

source("calculate_score_GW10.R")

source("plot_score_GW10.R")

## Co-expression enrichment analysis of dnLoF-ASD and dnMis-Epi genes during NPC transitions at GW16.

source("calculate_score_GW16.R")

source("plot_score_GW16.R")

## Co-expression enrichment analysis of dnLoF-ASD and dnMis-Epi genes during NPC transition at GW10 by downsampling.

source("calculate_downsample_GW10.R")

source("calculate_downsample_GW10_1.R")

source("plot_downsample_GW10.R")

## Co-expression enrichment analysis of dnLoF-ASD and dnMis-Epi genes during NPC transitions at GW16 by downsampling.

source("calculate_downsample_GW16.R")

source("calculate_downsample_GW16_1.R")

source("calculate_downsample_GW16_2.R")

source("calculate_downsample_GW16_3.R")

source("plot_downsample_GW16.R")

## Spearman’s correlation analysis of dnLoF-ASD and dnMis-Epi genes during NPC transition at GW10 by downsampling.

source("calculate_cor_GW10.R")

source("calculate_cor_GW10_1.R")

source("calculate_cor_GW10_2.R")

source("plot_cor_GW10.R")

## Spearman’s correlation analysis of dnLoF-ASD and dnMis-Epi genes during NPC transitions at GW16 by downsampling.

source("calculate_cor_GW16.R")

source("calculate_cor_GW16_1.R")

source("calculate_cor_GW16_2.R")

source("calculate_cor_GW16_3.R")

source("calculate_cor_GW16_4.R")

source("plot_cor_GW16.R")

## Examples of dnLoF-ASD gene pairs that show increased co-expression during the vRG-to-IPC transition at GW10 (vRG cells and IPCs combined) compared with vRG cells or IPCs alone.

source("plot_ASD_ADNP_CHD8.R")

source("plot_ASD_ANK2_SUV420H1.R")

source("plot_ASD_HECTD4_PHF3.R")

source("plot_ASD_KMT2A_SUV420H1.R")

## Examples of dnMis-Epi gene pairs that show increased co-expression during the vRG-to-IPC transition at GW10 (vRG cells and IPCs combined) compared with vRG cells or IPCs alone.

source("plot_Epi_DNM1_GABRB3.R")

source("plot_Epi_DNM1_KMT2B.R")

source("plot_Epi_FASN_KMT2B.R")

source("plot_Epi_FOXG1_RANGAP1.R")
