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Prerequisites​

We currently support pixelator running with Python 3.10, 3.11, 3.12, and 3.13.

This guide is primarily aimed at installing pixelator for use in downstream analysis. If you want to run the command-line parts of pixelator, we strongly recommend using the nf-core/pixelator pipeline. We also provide Docker images that package pixelator alongside all its necessary dependencies.

warning

Our software pixelator cannot be installed on macOS systems before Monterey (i.e. < 12) with an ARM chipset.

Installing Pixelator​

We always recommend installing pixelator in a separate environment (e.g. pna-analysis). Our preference is to install the Miniforge distribution of conda and mamba.

conda create -n pna-analysis python==3.13

Activate your recently created environment. In the next step, you will install pixelator.

conda activate pna-analysis

Python​

For our Python users, pixelator is easily installed via pip or conda:

pip3 install pixelgen-pixelator
warning

The pixelator version available in bioconda is not the latest. We recommend installing it via pip.

info

If you are installing pixelator from pip, you might need to install fastp as well.

This will create the pixelator command-line tool in your environment and make all methods available as a Python programming interface.

If you want to install a specific version of pixelator (e.g. 0.13.1 was the first released version), you can do the following:

pip3 install pixelgen-pixelator==0.13.1

You can see all available pixelator releases along with release notes here: https://github.com/pixelgentechnologies/pixelator/releases

Looking for an R package instead?​

If you prefer working in R instead of Python, we offer an R package called pixelatorR to analyze PNA data.