semvec/pypi-packages huggingface dataset:
pyudon 0.0.4
Unsupervised Discovery of Novel Disease Programs
Requires Python: >=3.10

# UDON: Unsupervised Discovery of Novel Disease Programs

**UDON** is a Python package for unsupervised discovery of disease subtypes from patient scRNA-seq data.  
It leverages **control-normalized pseudobulk expression** and **sparse NMF** to identify stable cell-state perturbations.  

UDON includes:  
- **SATAY-UDON** for metadata enrichment  
- **SASHIMI-UDON** for cohorts with limited controls *(coming soon!)*  

![Overview of UDON Toolkit](udon_toolkit_overview.png)
---

## 🚀 Installation  

Create a virtual environment and install UDON from PyPI:  

```bash
conda create -n udon_env python=3.10
conda activate udon_env

pip install py-udon
```

## 📂 Input Requirements  

UDON currently supports h5ad format and **human scRNA-seq data**.  

- If your data is in **Seurat**, convert it to `.h5ad` (AnnData) format using one of:  
  - [`SeuratDisk`](https://mojaveazure.github.io/seurat-disk/articles/convert-anndata.html)  
  - [`sceasy`](https://github.com/cellgeni/sceasy)  

- Alternatively, generate an AnnData object directly using **Scanpy**.  

- For **non-human datasets**, please reach out by opening a [GitHub issue](https://github.com/kairaveet/py-udon/issues). I’ll help set up the appropriate database for your species.  

---

## 🛠 Usage and Documentation  

1. **Download the database files**  
   - Download the database files attached as zip file [here](https://github.com/kairaveet/py-udon/blob/main/udon-python.zip). 
   - Please unzip the database folder and note the path to the folder and its contents. UDON requires access to this folder when running.  

2. **Run the example dataset**  
   - Download the example dataset: **SJIA cohort** ([GSE207633](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE207633))
   - Tutorial can be found at [`run_example_dataset.py`](https://github.com/kairaveet/py-udon/blob/main/run_example_dataset.py)

3. **Ensure input normalization**  
   UDON expects normalized expression values in `adata.X`.  
   - In a **Seurat object**:  
     ```R
     NormalizeData(object)
     ```  
   - In an **Scanpy h5ad**:  
     ```python
     sc.pp.normalize_total(adata, target_sum=1e4)
     sc.pp.log1p(adata)
     ```  

4. **Prepare donor metadata**  
   - UDON requires a donor-level metadata file.  
   - Example: [`donor_metadata.xlsx`](https://github.com/kairaveet/py-udon/blob/main/donor_metadata.xlsx)  
   - Make sure your metadata follows this structure.