HiCtool (v2.2)

• A/B compartment analysis.
• Calculation and plotting of the Pearson correlation matrix from the O/E contact matrix (only Yaffe-Tanay normalization method).
• Calculation and plotting of the eigenvector for A/B compartment annotation.
• Small bug fixes.

HiCtool (v2.1.1)

• Optimized pre-processing and normalization to allow the analysis of very high depth sequenced files.
• Added parameter to allow custom mapped reads filtering at the pre-processing step.
• Bedpe file generation step added for pre-processed read pairs.
• Deduplication step added in the pre-processing pipeline.
• Optimized and faster FEND file generation for adding GC content and mappability score.
• Small bug fixes.

HiCtool (v2.1)

• 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)

• 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.