easy-st

This repository contains tools that aim at simplifying and automating tasks in spatial transcriptomics on Linux. It contains the following:

• The file sr-helper.py is a Python script that simplifies the use of space ranger, a software tool that processes the raw data of Visium samples. Execute the command python3 sr-helper.py help for more information.
• The data directory contains sample data files that can be used with the processing pipelines. View the file inside of the directory to obtain the original reference.
• The pipelines directory comprises Jupyter notebooks that analyze spRNA-seq and scRNA-seq data using the scanpy and squidpy libraries.

To execute the notebooks, you'll need a Python virtual environment with the proper dependencies installed. Execute the following command to create the environment:

python3 -m venv venv
source venv/bin/activate
pip install -r requirements.txt

You can then launch Jupyter with this virtual environment and execute the notebooks of this repository.