hicue 0.4.0

A visualisation tool for Hi-C dataset.

HiCue

A visualization tool for Hi-C datasets that enables extraction, analysis, and visualization of chromatin interaction data.

Features

• Extract submatrices from Hi-C data around (pairs of) genomic positions
• Generate pileup visualizations of chromatin interactions
• Support for multiple file formats (BED, GFF, BigWig)
• Compare Hi-C datasets

Installation

pip install hicue

For development:

git clone https://github.com/Mae-4815162342/HiCue.git
cd HiCue
pip install -e .

Usage

Extract submatrices around genomic positions

hicue extract output_dir positions.bed data.cool

Generate pileup visualizations

hicue extract output_dir positions.bed data.cool --pileup

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Command Line Interface

HiCue provides several commands:

• extract: Extract submatrices around genomic positions
• extract2d: Extract submatrices for 2D genomic intervals
• tracks: Overlay genomic tracks on Hi-C visualizations
• compare: Compare two Hi-C datasets
• annotate: Annotate genomic positions with GFF features

Use hicue <command> --help for detailed options.

License

This project is licensed under CC BY-NC 4.0. See the LICENSE file for details.

Citation

If you use HiCue in your research, please cite:

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