8/12/24 DL

Scripts to analyze enrihcment of differential expression in
dynamic regions (e.g. regions within 10kb of sigDB, regions
within sigDC)

1_get_subsets.sh
	script to generate files containing different subsets of 
	genes and regions (e.g. regions containing DE gene, regions
	within 100kb of sigDB)

2A_count_regions.sh
	script to get counts of regions used in fold enrichment
	calulation

2B_count_genes.sh
	script to get counts of genes used in fold enrichment
	calculation

3_hypergeom_test.py
	performing hypergeometric test on fold enrichment of
	DE genes or DE regions in different subsets of dynamic
	reiongs

all_genes.bed
all_regions.bed
	files containing list of all regions or genes

bed/
	bed files with 10kb or 100kb bin coordinates

db_output/
	output from TGIF-DC

dc_output/
	output from TGIF-DB

de_output/
	output from DEseq

subsets/
	outputs from script 1

counts/
	outputs of script 2A and 2B

hypergeom/
	outputs from script 3

with_de_gene.py
within_100kb_of_sig_db.py
within_sig_dc.sh
within_tad_with_sig_db.py
	scripts to get different subset of dynamic regions,
	i.e., regions with DE gene, regions within 100kb of
	sigDB, within sigDC, or within TAD with at least 1
	sigDB. Wrapped and used by script 1 above
