Metadata-Version: 2.1
Name: stripecaller
Version: 0.1.0
Summary: Automated Stripe Identification from contact matrix.
Home-page: https://github.com/XiaoTaoWang/StripeCaller/
Author: XiaoTao Wang
Author-email: wangxiaotao686@gmail.com
License: UNKNOWN
Description: StripeCaller
        ============
        A Python implementation of the architectural stripe detecting algorithm described by Vian L et al [1]_.
        
        Currently, this package contains 3 scripts: *call-stripes*, *pileup-stripes* and *stripe-plot*:
        
        - call-stripes
          
          Call stripes from contact matrix. The only required input is the `cool <https://github.com/mirnylab/cooler>`_
          URI at certain resolution. The algorithm will detect horizontal (3') and vertical (5') stripes separately by
          searching for consecutive pixels with contact signals significantly higher than the local backgrounds. The output
          is a single file in bedpe format.
        
        - pileup-stripes
        
          This script performs a pileup analysis on stripes.
        
        - stripe-plot
        
          Visualize stripes on heatmap.
        
        
        Installation
        ============
        *stripecaller* is developed and tested on UNIX-like operating system, and following packages or softwares are
        required, which can be installed through `conda <Miniconda installer <https://conda.io/miniconda.html>`_
        
        a) Python 3.5+
        b) Multiprocess
        c) Numpy
        d) Scipy
        e) Matplotlib
        f) Cooler
        
        First, add some additional channels::
        
            $ conda config --add channels defaults
            $ conda config --add channels bioconda
            $ conda config --add channels conda-forge
        
        Then execute the following command::
        
            $ conda install multiprocess numpy scipy matplotlib cooler
        
        Finally, install the *stripecaller* by *pip*::
        
            $ pip install stripecaller
        
        Usage
        =====
        Open a terminal, type ``stripecaller -h`` for help information.
        
        
        Citation
        ========
        .. [1] Vian, L. et al. The Energetics and Physiological Impact of Cohesin Extrusion. Cell 175, 292-294, doi:10.1016/j.cell.2018.09.002 (2018).
Keywords: chromatin contact-matrix 3D genome stripe cooler
Platform: UNKNOWN
Classifier: Programming Language :: Python :: 3 :: Only
Classifier: License :: OSI Approved :: GNU General Public License v3 or later (GPLv3+)
Classifier: Operating System :: POSIX
Classifier: Development Status :: 4 - Beta
Classifier: Intended Audience :: Science/Research
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Description-Content-Type: text/x-rst
