• python2/3
• R
• (R package) riverplot
• (R package) ggplot2
• (R package) RColorBrewer
• (R package) amap
• (R package) gplots
• (R package) fastcluster
• (R package) doParallel
• (R package) foreach
• (R package) changepoint

Scripts to download, from ENCODE DCC, the ChIP-seq and ATAC-seq processed bam files of E10.5-P0 samples.

cd data_collection/
python get_files_from_DCC_ATAC.py
python get_files_from_DCC_ChIP.py

Running these two scripts will take ~1T space and several hours.

Plot the global mCG and mCH level of samples (Figure 1b and Figure 4a).

cd global_mCG_mCH/
Rscript plot_mC_trajectory.R

Riverplot showing CG-DMR classification (Figure 1e).

Rscript DMR_classification/plot_DMR_classification.R

Pie chart of proximal CG-DMRs (Extended Data Figure 2b)

Rscript DMR_classification/plot_prox_DMR_distr.R

mCG dynamics in tissue-specific CG-DMRs (Figure 2a-d).

Rscript mCG_dynamics/plot_barchart_merge.R
Rscript mCG_dynamics/plot_Heatmap_merge.R

mCG_dynamics/cluster_FB_DMR_H3K27ac.R is used to cluster forebrain-specific CG-DMRs with distinct mCG and H3K27ac dynamics during development into 8 groups. Two scripts below plot the mCG and H3K27ac profile of different classes of forebrain-specific CG-DMRs, and the correlation between mCG and H3K27ac in these CG-DMRs (Figure 2e-f).

Rscript mCG_dynamics/plot_Heatmap_H3K27ac_FB.R
Rscript mCG_dynamics/plot_H3K27ac_enrichment_FB_DMR.R

large_hypo_DMR/plot_lhDMR_epimark.R and large_hypo_DMR/plot_ovlp_SE.R are used to plot the intensity of epigenetic modification in large hypo- CG-DMRs, and the overlap between large hypo- CG-DMRs and super-enhancers (Figure 3b, c).

mCH_domain_calling/get_mCHdomain.pl and mCH_domain_calling/call_changepoint.R are scripts used to call mCH domains.

Scripts in mCH_domain_clustering/ are used to cluster mCH domains based on their mCH dynamics across tissues as well as visualization of the mCH dynamics of clustered mCH domain (Figure 4c and Extended Data Figure 7d).

WGCNA/run_WGCNA.R is used for performing WGCNA on RNA-seq data and clustering genes into co-expression modules.