Installation

To install the imaging-transcriptomics Python package you must first of all have Python v3.6+ installed on your system along with the pip package manager.

Tip

We suggest installing the package in a dedicated python environment using venv or conda depending on your personal choice. The installation on a dedicated environment avoids the possible clashes of dependencies after or during installation.

Note

All following steps assume that, if you have created a dedicated environment, this is currently active. If you are unsure you can check with which python from your terminal or activate your environment via the source activate (for conda managed environments) or source venv/bin/activate (for venv managed environments).

Before installing the imaging-transcriptomics package we need to install a package that is not available through PyPi but from GitHub only. This package is pypls and is used in the script to perform all PLS regressions. In order to install it you can run the following command from your terminal

pip install -e git+https://github.com/netneurolab/pypyls.git/#egg=pyls

This will install install the GitHub repository directly using pip and it will make it available with the name pyls.

Warning

Do not install pyls directly from pip with the command pip install pyls as this is a completely different package!

Once this package is installed you can install the imaging-transcriptomics package by running:

pip install imaging-transcriptomics

Once you get the message that the installation has completed you are set to go!