Installation#

Required Package#

BandHiC can be installed on Linux-like systems and requires the following dependencies:

  1. python >= 3.8

  2. numpy >= 1.24

  3. pandas >= 2.0

  4. scipy >= 1.10

  5. cooler >= 0.10

  6. hic_straw >= 1.3

  7. joblib >= 1.2

  8. numba >= 0.58

  9. matplotlib >= 3.7

There are two recommended ways to install BandHiC:

Option 1: Install via pip#

If you already have Python >= 3.8 installed:

pip install bandhic

If the installation fails due to dependency issues, please manually install the dependencies and then rerun the above command.

Option 2: Install from source with conda#

  1. Clone the repository

    git clone https://github.com/xdwwb/BandHiC-Master.git
cd BandHiC-Master

  2. Create the environment and activate it

    conda env create -f environment.yml
conda activate bandhic

  3. Install BandHiC

    pip install .

Optional dependency for .hic file support: hic-straw#

Support for reading .hic format Hi-C data relies on the third-party package hic-straw, which is not installed automatically with BandHiC.

If you do not need to read .hic files, you can ignore this dependency and use BandHiC normally.

If you do need .hic support, please install hic-straw manually using one of the following methods.

Method 1: Install via pip#

pip install hic-straw

Note that hic-straw includes native C/C++ extensions. Installation via pip may require a compatible compiler toolchain and system libraries (e.g. libcurl development headers).

Method 2: Install via Conda#

conda install -c bioconda hic-straw

Using Conda provides prebuilt binaries on many platforms and avoids local compilation issues.

Upstream installation guide#

For detailed, system-specific installation instructions, please refer to the official straw repository maintained by the Aiden Lab:

aidenlab/straw