Metadata-Version: 2.1
Name: scanpy-utils
Version: 0.1
Summary: Utility functions for scanpy
Home-page: https://github.com/NUPulmonary/scanpy-utils
Author: Nikolay Markov
Author-email: nikolay.markov@northwestern.edu
License: MIT
Project-URL: Documentation, https://scanpy-utils.readthedocs.io/
Project-URL: Changelog, https://scanpy-utils.readthedocs.io/en/latest/changelog.html
Project-URL: Issue Tracker, https://github.com/NUPulmonary/scanpy-utils/issues
Platform: UNKNOWN
Classifier: Development Status :: 4 - Beta
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: Unix
Classifier: Operating System :: POSIX
Classifier: Programming Language :: Python
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3 :: Only
Classifier: Programming Language :: Python :: 3.7
Classifier: Programming Language :: Python :: 3.8
Classifier: Programming Language :: Python :: 3.9
Classifier: Programming Language :: Python :: Implementation :: CPython
Classifier: Programming Language :: Python :: Implementation :: PyPy
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Requires-Python: >=3.7
Requires-Dist: scanpy (>=1.7.0)

========
Overview
========



Utility functions for `scanpy <https://scanpy.readthedocs.io>`_

* Free software: MIT license

Installation
============

::

    pip install scanpy-utils


Documentation
=============


See https://scanpy-utils.readthedocs.io/en/latest/reference/index.html


Development
===========

To run all the tests run::

    tox

Note, to combine the coverage data from all the tox environments run:

.. list-table::
    :widths: 10 90
    :stub-columns: 1

    - - Windows
      - ::

            set PYTEST_ADDOPTS=--cov-append
            tox

    - - Other
      - ::

            PYTEST_ADDOPTS=--cov-append tox


Changelog
=========

0.1 (2021-06-24) Initial release
--------------------------------

* ``get_markers`` function to extract markers from adata and add ``pct.1``, ``pct.2`` fields
* ``write_mtx`` function to dump adata in cellranger mtx format
* ``clean_metadata`` function to merge and remove duplicates from ``adata.var`` after merging

Plotting:

* ``feature_plot`` function to plot hexbin feature plot on UMAP
* ``plot_composition`` function to plot composition of clusters based on other metadata
* ``expr_colormap`` function with custom colormap for expression


