https://github.com/KenLauLab/dropkick

Automated cell filtering for single-cell RNA sequencing data
https://github.com/KenLauLab/dropkick

Last synced: 2 months ago
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Automated cell filtering for single-cell RNA sequencing data

• Host: GitHub
• URL: https://github.com/KenLauLab/dropkick
• Owner: KenLauLab
• License: mit
• Created: 2020-03-06T00:05:27.000Z (almost 5 years ago)
• Default Branch: master
• Last Pushed: 2023-11-14T01:07:02.000Z (about 1 year ago)
• Last Synced: 2024-10-02T14:18:22.571Z (3 months ago)
• Language: Python
• Size: 124 MB
• Stars: 24
• Watchers: 4
• Forks: 8
• Open Issues: 2
• Metadata Files:
  • Readme: README.rst
  • License: LICENSE

Awesome Lists containing this project

• awesome-single-cell - dropkick - [Python] - Automated cell filtering for single-cell RNA sequencing data. (Software packages / RNA-seq)

README

        
|Dropkick Logo|

|Latest Version|

Automated cell filtering for single-cell RNA sequencing data.

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

See our `Genome Research paper `_ for details on ``dropkick``'s guiding principles and validation.

----

``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, ``sudo apt install gfortran`` for Linux 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.

Full documentation is available at |KenLauLab.github.io/dropkick|_.

.. |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

.. |KenLauLab.github.io/dropkick| replace:: ``KenLauLab.github.io/dropkick``

.. _KenLauLab.github.io/dropkick: https://kenlaulab.github.io/dropkick/