Installation

We provide two ways to install the package of stereoAlign.

Please note that the current stereoAlign version offers full support of Linux operating system. Further version for other operating systems would be released soon.

1. Python

Install through Pypi.

pip install stereoAlign

or

git clone https://github.com/STOmics/stereoAlign.git

cd stereoAlign

python setup.py install

2. Anaconda

For convenience, we suggest using a separate conda environment for running stereoAlign. Please ensure Annaconda3 is installed.

Create conda environment and install stereoAlign package.

# create an environment called Spatialign
conda create -n stereoAlign python=3.8

# activate your environment
conda activate stereoAlign

# install package

pip install stereoAlign

or

git clone https://github.com/STOmics/stereoAlign.git

cd stereoAlign

python setup.py build

python setup.py install --user

#To use the environment in jupyter notebook, add python kernel for this environment.

pip install ipykernel

python -m ipykernel install --user --name=stereoAlign