Installation

STitch3D package is publicly available at https://github.com/YangLabHKUST/STitch3D.

STitch3D can be installed from PyPI:

pip install stitch3d

Alternatively, STitch3D can be downloaded from GitHub:

git clone https://github.com/YangLabHKUST/STitch3D.git
cd STitch3D
conda config --set channel_priority strict
conda env update --f environment.yml
conda activate stitch3d

After installation, the package can be imported in Python by:

import STitch3D

Software dependencies

python>=3.7
pytorch>=1.6.0, <=1.13.1
scanpy=1.7.2
anndata=0.7.6
pandas=1.1.5
numpy>=1.19.0
louvain=0.7.0
leidenalg>=0.7.0
umap-learn>=0.4.6
pot>=0.8.0
numba>=0.49.1
matplotlib<3.7