GIST

Leveraging Graph Information for Spatially Informed Patient Data Analysis with GIST

Create an environment if necessary

conda create -n gist python==3.10.0 r-base==4.3.1 -y
conda activate gist

Verify R home is in the conda environment

which R

/home/youruser/anaconda3/envs/gist/lib/R

install requirements

pip install -r requirements.txt

Install mclust packages

Rscript -e 'install.packages("mclust", repos="https://cran.r-project.org", type="source")'

install GIST packages

pip install git+https://github.com/gospelnnadi/GIST.git

run_GIST.py contains the GIST pipeline. python run_GIST.py &> output.log

Data Availability

The spatial transcriptomics datasets are available at: https://doi.org/10.5281/zenodo.15277298