STARK is a software for processing various types of single-cell Hi-C sequencing data, which currently includes the single-cell Hi-C technologies as follows:

• scHiC
• scHi-C+
• Dip-C
• HiRES
• sn-m3C
• scSPRITE
• sciHi-C
• snHi-C
• snHi-C
• scNanoHi-C
• scMethyl
• scCARE-seq

At the same time, we also provide a generalized way to process the sc3DG for details please see the tutorial.

To get started：

• Install STARK
• Read the documentation and see the Jupyter Notebook walkthrough.
• test data can be download form Zenodo
• Many more single-cell three dimension genome sequencing data are available on our website

We suggest creating a new python environment to install STARK before installation and STARK is based on python≥3.9.

stark can only be installed on the linux.

    conda create -n sc3dg python=3.9
    conda activate sc3dg
    git clone https://github.com/CCCKW/stark.git
    cd stark-main
    pip install -r requirements.txt
    python setup.py install

Attention: if you have any problem with installation of pysam, try to install the pysam as the follow command before run the 'pip install -r requirements.txt':

    conda install -c bioconda pysam

For usage and more detailed information of stark , you can visit the tutorial

Also, you can visit the scNucleome for more detailed information.