Metadata-Version: 1.2
Name: dropkick
Version: 1.2.4
Summary: Automated scRNA-seq filtering
Home-page: https://github.com/KenLauLab/dropkick
Author: Cody Heiser
Author-email: codyheiser49@gmail.com
License: UNKNOWN
Description: |Dropkick Logo|
        
        Automated cell filtering for single-cell RNA sequencing data.
        ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
        
        |Latest Version|
        
        ----
        
        ``dropkick`` works primarily with |scanpy|_'s ``AnnData`` objects, and accepts input files in ``.h5ad`` or flat (``.csv``, ``.tsv``) format. It also writes outputs to ``.h5ad`` files when called from the terminal.
        
        Installation via ``pip`` or from source requires a Fortran compiler (``brew install gcc`` for Mac users).
        
        Install from PyPI:
        ^^^^^^^^^^^^^^^^^^
        .. code:: bash
        
           pip install dropkick
        
        Or compile from source:
        ^^^^^^^^^^^^^^^^^^^^^^^
        .. code:: bash
        
           git clone https://github.com/KenLauLab/dropkick.git
           cd dropkick
           python setup.py install
        
        ----
        
        ``dropkick`` can be run as a command line tool or interactively with the
        |scanpy|_ single-cell analysis suite.
        
        Usage from command line:
        ^^^^^^^^^^^^^^^^^^^^^^^^
        
        .. code:: bash
        
           dropkick run path/to/counts.h5ad
        
        Output will be saved in a new ``.h5ad`` file containing cell probability
        scores, labels, and model parameters.
        
        You can also run the ``dropkick.qc`` module from terminal for a quick
        look at the total UMI distribution and ambient genes, saved as
        ``*_qc.png``:
        
        .. code:: bash
        
           dropkick qc path/to/counts.h5ad
        
        See |dropkick_tutorial.ipynb|_ for an
        interactive walkthrough of the ``dropkick`` pipeline and its outputs.
        
        .. |Dropkick Logo| image:: https://github.com/KenLauLab/dropkick/blob/master/data/dropkick_logo.png
        
        .. |Latest Version| image:: https://img.shields.io/pypi/v/dropkick
           :target: https://pypi.python.org/pypi/dropkick/
        
        .. |scanpy| replace:: ``scanpy``
        .. _scanpy: https://icb-scanpy.readthedocs-hosted.com/en/stable/
        
        .. |dropkick_tutorial.ipynb| replace:: ``dropkick_tutorial.ipynb``
        .. _dropkick_tutorial.ipynb: dropkick_tutorial.ipynb
        
Platform: UNKNOWN
Classifier: Programming Language :: Python :: 3
Classifier: Operating System :: OS Independent
Classifier: Intended Audience :: Developers
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: MIT License
Classifier: Topic :: Scientific/Engineering
Requires-Python: >=3.6
