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heirarchical TAD

The heirarchicalTAD folder has the code for generating enhancer-gene links from heirarchical TAD data taken from the source - https://www.cs.huji.ac.il/w~tommy/PSYCHIC/. All the 1e-4 bed files from this source are taken and then filtered on the basis of the tissue file before processing.

python heirarchicalTAD.py

Running the above command results in PSYCHIClinksDB enhancer-gene links file.

PSYCHIClinksDB

$ head PSYCHIClinksDB 
EH37E0105481	HUMAN|HGNC=15846|UniProtKB=Q9NP74	49	5.4e-14	4
EH37E0105482	HUMAN|HGNC=15846|UniProtKB=Q9NP74	49	5.4e-14	4
EH37E0105483	HUMAN|HGNC=15846|UniProtKB=Q9NP74	49	5.4e-14	4
EH37E0105484	HUMAN|HGNC=15846|UniProtKB=Q9NP74	49	5.4e-14	4
EH37E0105485	HUMAN|HGNC=15846|UniProtKB=Q9NP74	49	5.4e-14	4
EH37E0105486	HUMAN|HGNC=15846|UniProtKB=Q9NP74	49	5.4e-14	4
EH37E0105487	HUMAN|HGNC=15846|UniProtKB=Q9NP74	49	5.4e-14	4
EH37E0105509	HUMAN|HGNC=15846|UniProtKB=Q9NP74	49	4.1e-06	4
66387	HUMAN|HGNC=15846|UniProtKB=Q9NP74	49	4.1e-06	4
EH37E0105510	HUMAN|HGNC=15846|UniProtKB=Q9NP74	49	4.1e-06	4