Installation

We recommended installing the library within a separate conda environment running Python 3.10 or 3.11, python 3.12 is currently not supported.

conda create -n "scPortrait"
conda activate scPortrait
pip install git+https://github.org/MannLabs/scPortrait

For utilizing the stitching capabilities of scPortrait, a working java installation is required. If not already installed, you can download the latest version of Java from the official website or install it via mamba or conda:

conda install -c conda-forge openjdk

If you wish to utilize the accelerated stitching backend you need to install the graph-tool library. This library is not available via pip and needs to be installed seperately via conda.

conda install -c conda-forge graph-tool