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 frequency of interaction between two genes.
Test data: wgd_gene_calfreq.txt, chr_intra_matrix_bed.txt.
Download link of test file: https://github.com/yangxy2/3Dgenome-file/tree/main/web_test_file.
Input data description:
Gene pair list: The first row is the header; 14 columns, separated by tab; From left to right, each column represents gene 1 name, chromosome name, gene 1 start coordinate, gene 1 end coordinate, gene 2 name, chromosome name, gene 2 start coordinate, gene 2 end coordinate, gene 1 start bin id, gene 1 end bin id, the number of bins spanned by gene 1, gene 2 start bin id, gene 2 end bin id, the number of bins spanned by gene 2.
Interaction matrix: No header; 3 columns, separated by tab; From left to right, each column represents bin1 id, bin2 id, interaction frequency.