Installation

For Python users

The pipeline can be installed from the Python Package Index (PyPI) via the command line:

pip install hu-neuro-pipeline

Alternatively, to install the latest development version directly from GitHub:

pip install git+https://github.com/alexenge/hu-neuro-pipeline.git

The pipeline requires Python Version ≥ 3.8 and a number of dependency packages, which will get installed automatically when running the commands above.

For R users

First install reticulate and Miniconda for being able to import Python packages into R:

install.packages("reticulate")
reticulate::install_miniconda()

Then install the pipeline from the Python Package Index (PyPI):

reticulate::py_install("hu-neuro-pipeline", pip = TRUE)

Alternatively, to install the latest development version directly from GitHub:

reticulate::py_install("git+https://github.com/alexenge/hu-neuro-pipeline.git", pip = TRUE)

What next?

To jump right into how to use the pipeline, see Usage.

To learn about the different steps that the pipeline is carrying out, see Processing details.

If you have questions or need help with using the pipeline, please create an issue on GitHub.