Implementation of Gene Spatial Integration: enhancing spatial transcriptomics analysis via deep learing and batch effect mitigation.
Function explanation for the notebooks contained in Instruction.txt
Packages needed to be installed for Python environment are listed on python_requirements.txt
Packages needed to be installed for R environment are listed on r_dependencies.csv. Run R_install.r with Rscript to install from r_dependencies.csv
Rscript R_install.r
This repository also include BEER submodule that needs to be intialized. Use --recurse-submodules when cloning the repository or use 'git submodule update --init --recursive'
git clone --recurse-submodules https://github.com/Riandanis/Spatial_Integration_GSI.git
or
git clone https://github.com/Riandanis/Spatial_Integration_GSI.git
cd Spatial_Integration_GSI
git submodule update --init --recursive