Installation - SpatialRNA

SpatialRNA - A package that provides easier inferface to GNN models for single-molecule ST data analysis

Using Conda and pip¶

conda create -n dev-spatialrna
conda activate dev-spatialrna
conda install python=3.10.0

pip install torch==2.4.0 --index-url https://download.pytorch.org/whl/cu124

pip install torch_geometric==2.6.1

pip install pyg_lib torch_scatter torch_sparse torch_cluster torch_spline_conv -f https://data.pyg.org/whl/torch-2.4.0+cu124.html

pip install tqdm \
            scipy \
            scikit-learn \
            pandas \
            matplotlib \
            opencv-python

pip install spatialrna

References¶

Lyu, R., Vannan, A., Kropski, J. A., Banovich, N. E., & McCarthy, D. J. (2025). SpatialRNA: a python package for easy application of Graph Neural Network models on single-molecule spatial transcriptomics dataset. 10.1101/2025.03.20.644258