GITAR (Genome Interaction Tools and Resources) is a standardized, easy to use and flexible solution to manage Hi-C genomic interaction data, from processing to storage and visualization, composed of two modules: HiCtool and a processed data library.
GITAR has been published in Genomics, Proteomics & Bioinformatics (see article).
​If you use GITAR in your research, please cite the paper:

Calandrelli, R., Wu, Q., Guan, J., & Zhong, S. (2018). GITAR: An open source tool for analysis and visualization of Hi-C data. Genomics, proteomics & bioinformatics.
HiCtool (v2.1)
HiCtool is a Python library for processing, normalizing, and visualizing Hi-C data, including topological domain analysis.
Processed data library
Datasets from the 4DN Genome Interaction library processed using a standardized bioinformatic pipeline (HiCtool).
HiCtool v2.1 (05/20/2019)
  • HiCtool is now based only on unix commands. A Python script is given which contains utility functions for I/O of files generated with HiCtool in the Python console.
  • The entire pre-processing is now performed with a single-command.
  • Possibility of processing Hi-C data generated with a cocktail of restriction enzymes (i.e. as in the Arima Kit) or with restriction enzymes including "N" in their sequence.
  • HiCtool includes now additional species besides hg38 and mm10: hg19, mm9, dm6, susScr3, susScr11.
  • New function to visualize heatmaps from different samples or conditions on a side-by-side view for comparison.
  • Small bug fixes.
HiCtool v2.0 (03/28/2019)
  • HiCtool code is now hosted on GitHub.
  • Added inter-chromosomal analysis and visualization.
  • Included an additional global normalization method based on a matrix balancing approach.
  • New function to plot the all-by-all chromosomes global contact matrix.
  • Possibility of saving contact matrices in tab separated format.
  • Possibility of plotting topological domains over the heatmaps.
  • Small bug fixes.