WGD gene pair methylation level TADs boundary methylation level TADs boundary gene density Gene compartments judgment OE matrix generation Chromosome interaction-distance WGD gene pair contact score Gene pair contact frequency Conservative TADs analysis
TIPS

Function: Calculate the gene density around the boundary of TADs.
Test data: gene_TPM_pal.txt, TAD_list.txt, 60, 1000, 4.
Download link of test file: https://github.com/yangxy2/3Dgenome-file/tree/main/web_test_file.
Input data description:
Gene list: No header; 4 columns, separated by tab; From left to right, each column represents gene name, chromosome name, start coordinate, end coordinate; (The gene order is arranged according to the TPM expression level of the gene from low to high);
TADs list: No header; 3 columns, separated by tab; From left to right, each column represents chromosome name, start coordinate, end coordinate;
Window number: Number of windows around the TAD boundary (integer, half on left and right);
Window size: Size of each window(integer);
Group number: The number of groups according to the level of gene expression(integer).