🚀 Running Commands in each model Folder

This repository provides several scripts to run different models.
All commands should be executed inside the each model folder.

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📌 Available Scripts

Model	Script Location
scStyling	run_scStyling.sh
Simple Classifier	run_Simple_classifier.sh
SCAD	SCAD/model/run_SCAD.sh
SCAD (with foundation embeddings)	SCAD/model/run_SCAD.sh scFoundation/SCAD/model/run_SCAD_with_embeddings.sh
scDEAL (bulkmodel)	scDEAL/run_bulkmodel.sh
scDEAL (scmodel)	scDEAL/run_scmodel.sh

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⚙️ Command Arguments

All scripts take the following arguments:

• data_type

  • Options: Bulk, scStyleBulk
  • Specifies the type of input data.

• foundation_model

  • Options: gexpr, scRobust, scGPT, scFoundation
  • Defines whether to use raw gene expression (gexpr) or foundation model embeddings.

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Download Data

https://zenodo.org/records/17287489

🗂️ Dataset Tree (Markdown Links)

• data/

  • embeddings/
  • gexpr/

• SCAD/

  • data/

• scFoundation/

  • SCAD/
    • data/

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⚙️ Usage Example

# Clone the repository
git clone https://github.com/your-username/scStyling.git
cd scStyling

# Explore datasets
ls data/
ls SCAD/data/
ls scFoundation/SCAD/data/