Metadata-Version: 2.3
Name: biolearn
Version: 0.6.7.dev0+g1c6002b.d20241209
Summary: Machine learning for biomarkers computing
Author: Biolearn developers
Maintainer-email: Seth Paulson <sarudak@gmail.com>
License: License for biolearn
        =====================
        
        New BSD License
        
        Copyright (c) 2023 - 2023 The biolearn developers.
        All rights reserved.
        
        
        Redistribution and use in source and binary forms, with or without
        modification, are permitted provided that the following conditions are met:
        
          a. Redistributions of source code must retain the above copyright notice,
             this list of conditions and the following disclaimer.
          b. Redistributions in binary form must reproduce the above copyright
             notice, this list of conditions and the following disclaimer in the
             documentation and/or other materials provided with the distribution.
          c. Neither the name of the biolearn developers nor the names of
             its contributors may be used to endorse or promote products
             derived from this software without specific prior written
             permission.
        
        
        THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
        AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
        IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
        ARE DISCLAIMED. IN NO EVENT SHALL THE REGENTS OR CONTRIBUTORS BE LIABLE FOR
        ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
        DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
        SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
        CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
        LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
        OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
        DAMAGE.
Keywords: biomarker
Classifier: Intended Audience :: Developers
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: C
Classifier: Programming Language :: Python
Classifier: Programming Language :: Python :: 3.10
Classifier: Programming Language :: Python :: 3.11
Classifier: Topic :: Scientific/Engineering
Classifier: Topic :: Software Development
Requires-Python: >=3.10
Requires-Dist: appdirs
Requires-Dist: cvxpy
Requires-Dist: ecos
Requires-Dist: numpy>=1.19.0
Requires-Dist: openpyxl
Requires-Dist: pandas>=2.1.0
Requires-Dist: pyyaml
Requires-Dist: requests
Requires-Dist: scipy
Requires-Dist: xlrd
Provides-Extra: dev
Requires-Dist: black; extra == 'dev'
Requires-Dist: coverage; extra == 'dev'
Requires-Dist: flake8; extra == 'dev'
Requires-Dist: flake8-docstrings; extra == 'dev'
Requires-Dist: furo; extra == 'dev'
Requires-Dist: jupyterlab; extra == 'dev'
Requires-Dist: lifelines; extra == 'dev'
Requires-Dist: matplotlib>=3.3.0; extra == 'dev'
Requires-Dist: memory-profiler; extra == 'dev'
Requires-Dist: myst-parser; extra == 'dev'
Requires-Dist: numpydoc; extra == 'dev'
Requires-Dist: pytest-cov; extra == 'dev'
Requires-Dist: pytest>=6.0.0; extra == 'dev'
Requires-Dist: scikit-learn; extra == 'dev'
Requires-Dist: seaborn>=0.13.0; extra == 'dev'
Requires-Dist: sphinx; extra == 'dev'
Requires-Dist: sphinx-copybutton; extra == 'dev'
Requires-Dist: sphinx-design; extra == 'dev'
Requires-Dist: sphinx-gallery; extra == 'dev'
Requires-Dist: sphinxcontrib-bibtex; extra == 'dev'
Requires-Dist: sphinxext-opengraph; extra == 'dev'
Requires-Dist: torch; extra == 'dev'
Requires-Dist: torchvision; extra == 'dev'
Provides-Extra: doc
Requires-Dist: black; extra == 'doc'
Requires-Dist: coverage; extra == 'doc'
Requires-Dist: flake8; extra == 'doc'
Requires-Dist: flake8-docstrings; extra == 'doc'
Requires-Dist: furo; extra == 'doc'
Requires-Dist: lifelines; extra == 'doc'
Requires-Dist: matplotlib>=3.3.0; extra == 'doc'
Requires-Dist: memory-profiler; extra == 'doc'
Requires-Dist: myst-parser; extra == 'doc'
Requires-Dist: numpydoc; extra == 'doc'
Requires-Dist: seaborn>=0.13.0; extra == 'doc'
Requires-Dist: sphinx; extra == 'doc'
Requires-Dist: sphinx-copybutton; extra == 'doc'
Requires-Dist: sphinx-design; extra == 'doc'
Requires-Dist: sphinx-gallery; extra == 'doc'
Requires-Dist: sphinxcontrib-bibtex; extra == 'doc'
Requires-Dist: sphinxext-opengraph; extra == 'doc'
Provides-Extra: examples
Requires-Dist: lifelines; extra == 'examples'
Provides-Extra: plotting
Requires-Dist: matplotlib>=3.3.0; extra == 'plotting'
Requires-Dist: seaborn>=0.13.0; extra == 'plotting'
Provides-Extra: test
Requires-Dist: coverage; extra == 'test'
Requires-Dist: pytest-cov; extra == 'test'
Requires-Dist: pytest>=6.0.0; extra == 'test'
Description-Content-Type: text/x-rst

Biolearn
========

Biolearn enables easy and versatile analyses of biomarkers of aging data. It provides tools to easily load data from publicly available sources like the 
`Gene Expression Omnibus <https://www.ncbi.nlm.nih.gov/geo/>`_, `National Health and Nutrition Examimation Survey <https://www.cdc.gov/nchs/nhanes/index.htm>`_,
and the `Framingham Heart Study <https://www.framinghamheartstudy.org/>`_. Biolearn also contains reference implemenations for common aging clock such at the 
Horvath clock, DunedinPACE and many others that can easily be run in only a few lines of code. You can read more about it in our `paper <https://www.biorxiv.org/content/10.1101/2023.12.02.569722v2>`_.


.. warning::

    This is a prerelease version of the biolearn library. There may be bugs and interfaces are subject to change.


Important links
===============

- Source code: https://github.com/bio-learn/biolearn/
- Documentation Homepage: https://bio-learn.github.io/

Requirements
============

Python 3.10+

Install
=======
Install biolearn using pip.

.. code-block:: bash

    pip install biolearn

To verify the library was installed correctly open python or a jupyter notebook and run:

.. code-block:: python

    from biolearn.data_library import DataLibrary

If it executes with no errors then the library is installed. To get started check out `some code examples <https://bio-learn.github.io/auto_examples/index.html>`_

Discord server
==============

The biolearn team has a `discord server <https://discord.gg/wZH85WRTxN>`_ to answer questions,
discuss feature requests, or have any biolearn related discussions.

Issues
======

If you find any bugs with biolearn please create a Github issue including how we can replicate the issue and the expected vs actual behavior.


Contributing
============

Detailed instructions on developer setup and how to contribute are available `in the repo <https://github.com/bio-learn/biolearn/blob/master/DEVELOPMENT.md>`_