Datasets for ChromTransfer

This item contains the genomic data required for data preprocessing, model training, and prediction. Instructions for running and using the ChromTransfer model are available at https://github.com/TongjiZhanglab/ChromTransfer.
File descriptions
Regulatory.tar.gz
Contains two .h5 files with TF co-binding and chromatin context signals for 500-bp genomic regions with a 50-bp step size in mouse (mm10) and human (hg38). These files are required for ChromTransfer-Reg.FUNCODE.tar.gz
Contains two .pkl files with FUNCODE scores for genomic regions in mouse (mm10) and human (hg38). These files are required for ChromTransfer-Cons and ChromTransfer-Reg.DNA.tar.gz
Contains DNA sequences for genomic regions in mouse (mm10) and human (hg38). These files are required for ChromTransfer-Base, ChromTransfer-Cons, and ChromTransfer-Reg.regions.tar.gz
Contains BED files defining genomic regions in mouse (mm10) and human (hg38). These files are used to generate training, validation, and test datasets.cobinding_TF_source.tar.gz
Contains TF co-binding and interaction information in mouse and human. These files are used to identify co-binding TFs for a given TF not included in the predefined TF list.demo.tar.gz
Contains example files demonstrating data preprocessing, model training, and prediction on mouse and human genomes.