pytrance 0.1.0

pyTrance: framework for subcellular spatial transcriptomics analysis

pyTrance

A Python framework for transcript co-localization analysis based on latent embeddings for imaging-based spatial transcriptomics data.

Have a look at our preprint and documentation for more details.

Installation

First, download the code to your desired location in your filesystem:

git clone https://github.com/rajewsky-lab/pytrance/
cd pytrance

To install the pyTrance dependencies we highly recommend using mamba as a fast, drop-in replacement for conda. Alternatively, replace mamba with conda in the command bellow.:

mamba env create -f environment.yaml
conda activate pytrance

For the installation of PyTorch please follow the instructions on the PyTorch website to make sure it is compatible with the CUDA version on your machine.

Finally, install pyTrance:

pip install pytrance