Delta score calculation and correlation

1. bigwig_to_bedgraph.sh: Map scores to 10kb bins.
2. bedgraph_deltas.sh: Calculate delta scores between normalized ChIP-seq bedgraphs.
3. delta_plot.R: Plot delta values in a scatterplot.

Genomewide bigwig correlation scatter plots

1. multi_bigwig_compare.sh: Using deepTools for genome-wide correlation of normalized ChIP-seq.
2. bigwig_correlation_scatterplots.R: Plotting pairwise scatterplots between all samples.

Enrichment by genomic region

1. plot_chip_ratio.R: Plot ratio of real:expected ChIP-seq reads at annotated genomic regions of interest.

DNMT3A1 enrichment tests

1. bigwigToBedgraph.sh: Map scores to 10kb bins.
2. shuffle_regions.sh: Permute CGIs genome-wide to get a set of comparison regions.
3. permutation_analysis.R: Plot DNMT3A scores across CGIs and permuted regions.

H3K36me2-ranked intergenic region plots

1. bigwig_to_bedgraph.sh: Map scores to 10kb bins.
2. score_per_igr.sh: Compute average score per IGR.
3. dnmt3a_across_ranked_IGRs.R: Plot DNMT3A scores across IGRs, ranked by H3K36me2.