spatialrna 0.2.0

A package for spatial RNA graph data processing and analysis.

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

Pre-requisite packages installation

## Using Conda and pip

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

## torch 2.4.0 cuda version 12.4
pip install torch==2.4.0 --index-url https://download.pytorch.org/whl/cu124

## torch_geometric=2.6.1 https://pytorch-geometric.readthedocs.io/en/stable/install/installation.html#installation-via-pypi

pip install torch_geometric==2.6.1

## Additional useful libraries https://pytorch-geometric.readthedocs.io/en/stable/install/installation.html#additional-libraries

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

## clustering and plotting requires

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

Install spatialrna

pip install spatialrna

Documentations

https://ruqianl.github.io/spatialrna_docs/