spotiphy 0.1.0

An integrated pipeline designed to deconvolute and decompose spatial transcriptomics data, and produce pseudo single-cell resolution images.

Spotiphy reveals location-specific cell subtypes through transcriptome profile at single-cell resolution

Usage and Tutorials

Tutorials of spotiphy can be found in folder Tutorials.

Installation

To install Spotiphy, it is recommended to create a separate conda environment. This approach helps to manage dependencies and avoid conflicts with other packages.

conda create -n Spotiphy-env python=3.9
conda activate Spotiphy-env

Spotiphy is built based on Pytorch. Although installing Spotiphy automatically includes PyTorch, it is recommended that users manually install PyTorch (link) to allow for more flexibility, particularly for those who wish to utilize CUDA capabilities. We offer two methods for installing the Spotiphy package:

• Install from GitHub: This method allows you to install the latest version directly from the source code hosted on GitHub.

pip install git+https://github.com/jyyulab/Spotiphy.git

• Install from PyPI using pip: This approach is for installing the Spotiphy package from the Python Package Index (PyPI), which is more streamlined for users who prefer standard package installations.

pip install spotiphy

To test the Installation, try to import Spotiphy in Python.

import spotiphy

Cite Spotiphy:

If you have questions, please contact the authors of the method:

• Ziqian Zheng - [e-mail]
• Jiyuan Yang - [e-mail]