Installation

From PyPI

You can install mepylome directly from PyPI using pip:

pip install mepylome

From Source

If you want the latest version, you can download mepylome directly from the source:

git clone https://github.com/brj0/mepylome.git && cd mepylome && pip install .

CNV Segments

To perform segmentation on the CNV plot (horizontal lines identifying significant changes), additional packages are required. These packages depend on a C compiler. Follow the instructions below to install them based on your Python version.

Python Versions Below 3.10

For Python < 3.10, install the necessary packages using the following command:

pip install cython
pip install ailist==1.0.4
pip install cbseg

If you encounter any compatibility issues, you may need to downgrade numpy to version 1.26.4. Make sure you have a C compiler installed on your system to build this package.

Python 3.10 and Later

For Python 3.10 and Later, you can install the linear_segment package instead. Use the following command:

pip install linear_segment

Make sure you have a C compiler installed on your system to build this package.

Alternative Package

As an alternative, you can try installing the ruptures package, which provides similar functionality. Its probably the fastes package. To install, use:

pip install ruptures

Important Note

Only one of the above packages should be installed at a time to avoid conflicts.

Uninstallation

To uninstall Mepylome:

Run:
```
pip uninstall mepylome
```
Delete the following directories:
- ~/.cache/mepylome (Contains cached files)
- ~/mepylome (Contains tutorial/example files)

Platform Compatibility

This package is written for Linux and has been tested under Ubuntu.

Warning

Windows users may encounter issues with the pyranges package, which affects CNV calculation, making it not possible to perform CNV calculations on Windows directly. However, apart from CNV calculations, other functionalities of the package should work on Windows.

To overcome this limitation, Windows users are advised to use Windows Subsystem for Linux (WSL).