StHistDDComp

# StHistDDComp

### _Spatial Transcriptomics Histology-based Domain Detection Comparison_

—

## Overview

Currently, the repository supports and integrates the following methods:

1.  [stLearn](https://github.com/BiomedicalMachineLearning/stLearn)
2.  [SpaGCN](https://github.com/jianhuupenn/SpaGCN)
3.  [conST](https://github.com/ys-zong/conST)
4.  [DeepST](https://github.com/JiangBioLab/DeepST)
5.  [ScribbleDom](https://github.com/1alnoman/ScribbleDom)

Each method is wrapped with a uniform interface for running experiments, saving results, and ensuring reproducibility across random seeds.

—

## Repository Structure

“`txt
    StHistDDComp/
    │
    ├── README.md
    ├── conST_run/                 # Runner and setup scripts for conST
    │   ├── README.md
    │   ├── run_20.py
    │   └── setup_conST_run.sh
    ├── datasets/                  # Dataset folder (DLPFC, HBC, etc.)
    │   └── …
    ├── DeepST_run/                # Runner and setup scripts for DeepST
    │   ├── README.md
    │   ├── config.json
    │   ├── run_20.py
    │   └── setup_DeepST_run.sh
    ├── results/                   # Output folder for domain labels and metrics
    ├── run_analysis/              # Analysis scripts for metrics and visualization
    │   ├── config.json
    │   └── wilcox.py
    ├── ScribbleDom_run/           # Runner and setup scripts for ScribbleDom
    │   ├── README.md
    │   ├── config.json
    │   ├── run_20.py
    │   ├── ScribbleDom_run.py
    │   └── setup_ScribbleDom_run.sh
    ├── SpaGCN_run/                # Runner and setup scripts for SpaGCN
    │   ├── README.md
    │   ├── config.json
    │   ├── run_20.py
    │   └── setup_SpaGCN_run.sh
    └── stLearn_run/               # Runner and setup scripts for stLearn
        ├── README.md
        ├── config.json
        ├── run_20.py
        └── setup_stLearn_run.sh
“`

—

## Setup Instructions

### 1. Clone the repository

“`bash
git clone https://github.com/asifajrof/StHistDDComp.git
cd S