Epical is coded in Python. It needs Python 3 (version 3.5.x) or a later version for installation and execution.
- Python 3
- pip3
- R
- TensorFlow (Only requires by AltumAge)
Note
Users do NOT need to install these packages manually, as they will be automatically installed if you use pip3.
# 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.
$ pip3 install epical --upgrade
$ pip3 uninstall epical
Print out usage and all the available clocks
$ epical --help
usage: epical [-h] [-v]
{Horvath13, Horvath13_shrunk, Horvath18, Levine, ...}
...
# 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 ...