/stark

Primary LanguageC

STARK tutorial

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

Installation

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.