A transformer method of reconstructing 3D structures of genomes and chromosomes from Hi-C data
The directory contains the code used to run the experiments and our own models for the paper
The Cooler file dataset for Human cells with GEO number GSE130711 can be get from https://salkinstitute.app.box.com/s/fp63a4j36m5k255dhje3zcj5kfuzkyj1 or more detailed Human single-cell data at https://salkinstitute.app.box.com/s/fp63a4j36m5k255dhje3zcj5kfuzkyj1/folder/82405563291
The Cooler file format dataset for Drosophila was obtained from GEO with code GSE131811 can be get from https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE131811
HiCDFormer is written in Python3 and uses the Pytorch module. The dependencies can be installed by the following command:
# create conda environment
conda env create -f HiCFormer.yml
# active the environment
conda active HiCFormer# First step create folder for the datasets, the 'Datasets' folder should be at the same level as 'TrainingYourData' Folder
mkdir -p Datasets/Human
# or
mkdir -p Datasets/Drosophila
# Second download the dataset to Datasets/Human or Datasets/Drosophila the by the given link
# Third check the download files' extension, if not .mcool extension, you should zoomify the files to get the resolution you want
cooler zoomify --balance filename.cool
# Fourth name the zoomified file to the customized name as bellow
mv fiilename.mcool cell1_name.mcool
# note: you can replace the numerical number as any interger you want, and change the 'name' as you want.If you want to retrain your dataset, YOU can run HiCFormer by the following command:
If you want to retrain your dataset, YOU can run HiCFormer by the following command:
Yanli Wang
Deparment of Computer Science
University of Missouri
Columbia, MO 65211, USA
Email: yw7bh@missouri.edu
Jianlin (Jack) Cheng, PhD
William and Nancy Thompson Distinguished Professor
Department of Electrical Engineering and Computer Science
University of Missouri
Columbia, MO 65211, USA
Email: chengji@missouri.edu