Metadata-Version: 2.1
Name: pimkl
Version: 0.1.1
Summary: pathway induced multiple kernel learning for computational biology
Home-page: https://github.com/PhosphorylatedRabbits/pimkl
Author: Joris Cadow and Matteo Manica
Author-email: joriscadow@gmail.com, drugilsberg@gmail.com
License: MIT license
Keywords: pimkl
Platform: UNKNOWN
Classifier: Development Status :: 2 - Pre-Alpha
Classifier: Intended Audience :: Developers
Classifier: License :: OSI Approved :: MIT License
Classifier: Natural Language :: English
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.5
Classifier: Programming Language :: Python :: 3.6
Classifier: Programming Language :: Python :: 3.7
Requires-Python: >=3.5
Requires-Dist: numpy (>=1.14.0)
Requires-Dist: scipy (>=1.0.0)
Requires-Dist: pandas (>=0.22.0)
Requires-Dist: scikit-learn (>=0.18.1)
Requires-Dist: networkx (>=2.1)
Requires-Dist: statsmodels (>=0.8.0)
Requires-Dist: seaborn (>=0.8.1)
Requires-Dist: Click (>=7.0)
Requires-Dist: tqdm (>=4.36.1)

=====
pimkl
=====


.. .. image:: https://travis-ci.org/PhosphorylatedRabbits/pimkl.svg
    :target: https://travis-ci.org/PhosphorylatedRabbits/pimkl

.. .. image:: https://readthedocs.org/projects/pimkl/badge/?version=latest
        :target: https://pimkl.readthedocs.io/en/latest/?badge=latest
        :alt: Documentation Status

.. .. image:: https://pyup.io/repos/github/PhosphorylatedRabbits/pimkl/shield.svg
     :target: https://pyup.io/repos/github/PhosphorylatedRabbits/pimkl/
     :alt: Updates



pathway induced multiple kernel learning for computational biology


* Free software: MIT license
* Documentation: https://pimkl.readthedocs.io.


Features
--------

The pimkl command:

.. code-block:: console

    Usage: pimkl [OPTIONS] NETWORK_CSV_FILE NETWORK_NAME GENE_SETS_GMT_FILE
             GENE_SETS_NAME PREPROCESS_DIR OUTPUT_DIR CLASS_LABEL_FILE [LAM]
             [K] [NUMBER_OF_FOLDS] [MAX_PER_CLASS] [SEED] [MAX_PROCESSES]
             [FOLD]

    Console script for a complete pimkl pipeline, including preprocessing and
    analysis. For more details consult the following console scripts, which
    are here executed in this order. `pimkl-preprocess --help` `pimkl-analyse
    run-performance-analysis --help`

    Options:
    -fd, --data_csv_file PATH       [required]
    -nd, --data_name TEXT           [required]
    --model_name [EasyMKL|UMKLKNN|AverageMKL]
    --help                          Show this message and exit.

Requirements
-------------

* C++14 capable C++ compiler
* cmake (>3.0.2)
* Python


Installation
-------------

Install the dependencies

.. code-block:: bash

    pip install -r requirements.txt

Install the package

.. code-block:: bash

    pip install .


Tutorial
---------

You can find a brief tutorial in the dedicated folder.

Credits
-------

This package was created with Cookiecutter_ and the `audreyr/cookiecutter-pypackage`_ project template.

.. _Cookiecutter: https://github.com/audreyr/cookiecutter
.. _`audreyr/cookiecutter-pypackage`: https://github.com/audreyr/cookiecutter-pypackage


=======
History
=======

0.1.0 (2020-11-05)
------------------

* First release on PyPI.

0.1.0 (2019-10-01)
------------------

* First release.


