========================
FAN-C command line tools
========================

The ``fanc`` tool should be accessible from the command line after you installed FAN-C
(see :ref:`fanc_installation`).
It provides convenient commands for the generation, modification, and analysis of Hi-C data.

.. toctree::
   :maxdepth: 2

    Overview and shared parameters <fanc-executable/fanc_basic>
    Working with Cooler, Juicer, and text files <fanc-executable/compatibility>
    Generate Hi-C matrices <fanc-executable/fanc_generate_hic>
    Analyse Hi-C matrices <fanc-executable/fanc_analyse_hic>
