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.

Warning

At current time Python versions 3.9+ are not fully supported as there

are some issue during the installation of the Numpy version used by the toolbox in these versions of Python.

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!

A second package to install for the full functionalities of the imaging-transcriptomics toolbox is the ENIGMA toolbox . To install this we’ll follow the instructions of the developers. In brief, install this by running the commands:

git clone https://github.com/MICA-MNI/ENIGMA.git
cd ENIGMA
python setup.py install

Once these packages 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!

Note

The version v1.0.0 and v1.0.1, can cause some issues on the installation due to compatibility issues of some packages. In version v1.0.2+ this issue has been resolved during installation. If you have one of the older versions installed you might want to update the version using the command pip install --upgrade imaging-transcriptomics.

Note

From version v1.1.0 has the possibility of running directly from the toolbox also the gene set enrichment analysis (GSEA). Version v1.1.8 has a major speedup in the correlation analyses, reducing the overall time needed to run the analysis.