| Name | epical JSON |
| Version |
1.1.0
JSON |
| download |
| home_page | None |
| Summary | epical --- Epigenetic age Calculator |
| upload_time | 2024-04-21 02:35:39 |
| maintainer | None |
| docs_url | None |
| author | None |
| requires_python | >=3.8 |
| license | Copyright (c) 2024 The Python Packaging Authority Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. |
| keywords |
epigenetics age
biological age
dna methylation
methylationepic
850k
450k
rrbs
wgbs
|
| VCS |
 |
| bugtrack_url |
|
| requirements |
No requirements were recorded.
|
| Travis-CI |
No Travis.
|
| coveralls test coverage |
No coveralls.
|
.. image:: https://readthedocs.org/projects/ansicolortags/badge/?version=latest
:target: https://epical.readthedocs.io/?badge=latest
.. image:: https://img.shields.io/badge/Maintained%3F-yes-green.svg
:target: https://GitHub.com/Naereen/StrapDown.js/graphs/commit-activity
.. image:: https://img.shields.io/badge/Made%20with-Python-1f425f.svg
:target: https://www.python.org/
.. image:: https://img.shields.io/badge/Made%20with-Sphinx-1f425f.svg
:target: https://www.sphinx-doc.org/
Installation
=============
*Epical* is coded in Python. It needs Python 3 (version 3.5.x) or a later
version for installation and execution.
Prerequisites
--------------
- `Python 3 <https://www.python.org/downloads/>`_
- `pip3 <https://pip.pypa.io/en/stable/installing/>`_
- `R <https://www.r-project.org/>`_
- `TensorFlow <https://www.tensorflow.org/>`_ (Only requires by *AltumAge*)
Python Dependencies
--------------------
- `pandas <https://pandas.pydata.org/>`_
- `numpy <http://www.numpy.org/>`_
- `scipy <https://www.scipy.org/>`_
- `sklearn <https://www.scilearn.com/>`_
- `bx-python <https://github.com/bxlab/bx-python>`_
- `matplotlib <https://matplotlib.org/>`_
- `EpigeneticPacemaker <https://epigeneticpacemaker.readthedocs.io/en/latest/>`_
.. note::
Users do NOT need to install these packages manually, as they will be
automatically installed if you use
`pip3 <https://pip.pypa.io/en/stable/installing/>`_.
Install Epical
--------------
::
# Create a virtual environment ...
# install from PyPI
$ pip3 install epical
# install from github
$ pip3 install git+https://github.com/liguowang/epical.git
# test if *epical* is available and excutable
$ epical --version
epical 0.0.1
.. note::
If you used Python virtual environment to install
`TensorFlow <https://www.tensorflow.org/>`_, you need to run the
above command in the same virtual environment.
Upgrade *Epical*
-----------------
::
$ pip3 install epical --upgrade
Uninstall *Epical*
-------------------
::
$ pip3 uninstall epical
Run *Epical*
============
Print out usage and all the `available clocks <https://epical.readthedocs.io/en/latest/overview.html#available-clocks>`_
-------------------------------------------------------------------------------------------------------------------------
::
$ epical --help
usage: epical [-h] [-v]
{Horvath13, Horvath13_shrunk, Horvath18, Levine, ...}
...
Example: run the "Horvath13" command
-------------------------------------
::
# print usage of the "Horvath13" command
$ epical Horvath13 --help
...
# run example data
$ epical Horvath13 -m blood_N20_info.tsv -o output blood_N20_MethylationEPIC-v1.0_beta.tsv.gz
2024-01-04 07:52:11 [INFO] The prefix of output files is set to "output".
2024-01-04 07:52:11 [INFO] Loading Horvath13 clock data ...
2024-01-04 07:52:11 [INFO] Clock's name: "Horvath13"
2024-01-04 07:52:11 [INFO] Clock was trained from: "Pan-tissue"
2024-01-04 07:52:11 [INFO] Clock's unit: "years"
2024-01-04 07:52:11 [INFO] Number of CpGs used: 353
...
Documentation
==============
`https://epical.readthedocs.io/en/latest/ <https://epical.readthedocs.io/en/latest/>`_
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