liguowang / epical

A repository of epigenetic age calculators

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
• pip3
• R
• TensorFlow (Only requires by AltumAge)

Python Dependencies

• pandas
• numpy
• scipy
• sklearn
• bx-python
• matplotlib
• EpigeneticPacemaker

Note

Users do NOT need to install these packages manually, as they will be automatically installed if you use pip3.

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, 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

$ 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/