SVC

SVC is a Vision Transformer-based Spatial Virtual Cell Model for Deciphering Subcellular Spatial Transcriptomic Heterogeneity.

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Installation

1. Clone the repository

git clone https://github.com/aster-ww/SVC.git
cd SVC

2. Create the conda environment

conda env create -f environment.yml
conda activate SVC

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Documentation

Full documentation and tutorials are available on readthedocs page

The documentation includes:

• Project overview
• Installation instructions
• API reference
• Data preprocessing
• Model usage examples

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Data availability

Example datasets used in this project are publicly available:

• SeqFISH+

• MERFISH

• Xenium human breast cancer

• Xenium mouse brain

• Xenium Prime 5K mouse brain hemishpere

Processed data, saved checkpoints, and main outputs used in our project can be downloaded via https://drive.google.com/drive/folders/1G4Nl-As6hXsAh7vHaRJ3vkYv44A-mU5f.

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Visit our group website for more statistical tools on analyzing genetics, genomics and transcriptomics data.