Any genomic contact map can be seen as an adjacency matrix, and thus a natural representation for a graph. Despite this fact, contact maps are hardly ever analyzed as graphs. Probably the main reasons for this is the difficulty in handling these huge sparse matrices.
HiCONA is a Python package whose aim is to provide the tools to perform network analysis on genomic contact maps. HiCONA provides functionalities for I/O, graph creation and manipulation, plotting and overall a customizable interface which can be used with the provided methods or user-defined ones.
HiCONA requires Python ≥3.10 and is supported on Linux and macOS only. This is due to the required dependency graph-tool. For the same reason, installation through conda-forge is recommended (the usage of mamba instead of conda is strongly advised for faster dependency solving).
conda create -n hicona_env
conda activate hicona_env
conda install -c conda-forge hiconaInstallation through pip is also possible, though an available installation of graph-tool in the environment is required.
pip install hiconaInstallation from source (mainly for development purposes) is possible using the provided environment.yaml file.
git clone git@github.com:leomorelli/HiCONA.git hicona
cd hicona
conda env create -f environment.yaml
conda activate hicona_envAPI documentation and examples will soon be available on ReadTheDocs.
Reference to the publication will be available soon. For the time being, if you find this package useful, please cite it by providing the link to this page.
Contributing guidelines will be available soon.