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Python Reimplementation of the soupx scRNA ambient removal package

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# SoupX Python

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A Python implementation of SoupX for removing ambient RNA contamination from droplet-based single-cell RNA sequencing data.
 
## Overview

Droplet-based single-cell RNA sequencing (scRNA-seq) experiments contain ambient RNA contamination from cell-free mRNAs present in the input solution. This "soup" of background contamination can significantly confound biological interpretation, particularly in complex tissues where contamination rates can exceed 20%.

SoupX addresses this by:
1. **Estimating** the ambient RNA expression profile from empty droplets
2. **Quantifying** contamination fraction in each cell using marker genes  
3. **Correcting** cell expression profiles by removing estimated background

This Python implementation maintains full compatibility with the original R package interface while integrating seamlessly with the Python scRNA-seq ecosystem (scanpy, anndata).

## Background & Citation

This implementation is based on the method described in:

> **Young, M.D., Behjati, S.** SoupX removes ambient RNA contamination from droplet-based single-cell RNA sequencing data. *GigaScience* 9, giaa151 (2020). [https://doi.org/10.1093/gigascience/giaa151](https://doi.org/10.1093/gigascience/giaa151)

**Please cite the original paper if you use this implementation in your research.**

## Installation

### From PyPI (Recommended)

```bash
pip install soupx-python
```

### From Source

```bash
git clone https://github.com/NiRuff/soupx-python.git
cd soupx-python
pip install -e .
```

### Dependencies

- Python ≥3.8
- numpy ≥1.19.0
- pandas ≥1.2.0
- scipy ≥1.6.0
- statsmodels ≥0.12.0
- scanpy ≥1.7.0 (optional, for integration examples)

## Quick Start

### Basic Usage (R-compatible interface)

```python
import soupx

# Load 10X data (cellranger output directory)
sc = soupx.load10X("path/to/cellranger/outs/")

# Automatically estimate contamination
sc = soupx.autoEstCont(sc)

# Generate corrected count matrix
corrected_counts = soupx.adjustCounts(sc)
```

### Integration with scanpy

```python
import scanpy as sc
import soupx
import pandas as pd

# Load raw 10X data with both filtered and raw counts
adata_raw = sc.read_10x_mtx("path/to/raw_feature_bc_matrix/", cache=True)
adata_filtered = sc.read_10x_mtx("path/to/filtered_feature_bc_matrix/", cache=True)

# Create SoupChannel
soup_channel = soupx.SoupChannel(
    tod=adata_raw.X.T.tocsr(),    # raw counts (genes × droplets)
    toc=adata_filtered.X.T.tocsr(), # filtered counts (genes × cells)
    metaData=pd.DataFrame(index=adata_filtered.obs_names)
)

# Add clustering information (essential for good results)
sc.tl.leiden(adata_filtered, resolution=0.5)
soup_channel.setClusters(adata_filtered.obs['leiden'].values)

# Estimate and remove contamination
soup_channel = soupx.autoEstCont(soup_channel, verbose=True)
corrected_matrix = soupx.adjustCounts(soup_channel)

# Replace counts in AnnData object
adata_corrected = adata_filtered.copy()
adata_corrected.X = corrected_matrix.T  # Convert back to cells × genes

# Continue with standard scanpy workflow
sc.pp.highly_variable_genes(adata_corrected)
sc.tl.pca(adata_corrected)
# ... further analysis
```

## Advanced Usage

### Manual Contamination Estimation

For experiments where automatic estimation fails or when you have prior biological knowledge:

```python
# Manually specify contamination fraction
soup_channel.set_contamination_fraction(0.10)  # 10% contamination

# Or use specific marker genes (e.g., hemoglobin genes for tissue samples)
hemoglobin_genes = ['HBA1', 'HBA2', 'HBB', 'HBD', 'HBG1', 'HBG2']
non_expressing = soupx.estimateNonExpressingCells(
    soup_channel, 
    hemoglobin_genes,
    clusters=soup_channel.metaData['clusters'].values
)

# Calculate contamination using marker genes
soup_channel = soupx.calculateContaminationFraction(
    soup_channel, 
    {'HB': hemoglobin_genes}, 
    non_expressing
)
```

### Method Selection

```python
# Different correction methods available:

# 1. Subtraction (default, fastest)
corrected = soupx.adjustCounts(soup_channel, method="subtraction")

# 2. Multinomial (most accurate, slower)
corrected = soupx.adjustCounts(soup_channel, method="multinomial")

# 3. SoupOnly (removes only confidently contaminated genes)
corrected = soupx.adjustCounts(soup_channel, method="soupOnly")

# Round to integers (some downstream tools require this)
corrected = soupx.adjustCounts(soup_channel, roundToInt=True)
```

## API Reference

### Core Classes

#### `SoupChannel`
Main container for scRNA-seq data and contamination analysis.

**Parameters:**
- `tod`: Raw count matrix (genes × droplets, sparse)
- `toc`: Filtered count matrix (genes × cells, sparse)  
- `metaData`: Cell metadata DataFrame
- `calcSoupProfile`: Whether to estimate soup profile automatically (default: True)

#### Key Methods

##### `autoEstCont(sc, **kwargs)`
Automatically estimate contamination fraction using marker genes.

**Parameters:**
- `tfidfMin`: Minimum tf-idf for marker genes (default: 1.0)
- `soupQuantile`: Quantile threshold for soup genes (default: 0.9)
- `verbose`: Print progress information (default: True)

##### `adjustCounts(sc, **kwargs)`
Remove contamination and return corrected count matrix.

**Parameters:**
- `method`: Correction method ("subtraction", "multinomial", "soupOnly")
- `roundToInt`: Round results to integers (default: False)
- `clusters`: Cluster assignments (improves accuracy)

### Utility Functions

##### `load10X(dataDir)`
Load 10X CellRanger output directory.

##### `quickMarkers(toc, clusters, N=10)`
Identify cluster marker genes using tf-idf.

## Validation & Benchmarking

This implementation has been validated against the original R version using:

- **Species-mixing experiments**: Cross-species contamination quantification
- **PBMC datasets**: Standard benchmark with known marker genes
- **Complex tissue samples**: Kidney tumor and fetal liver data

Key validation results:
- Contamination estimates: R² > 0.95 correlation with R implementation
- Correction accuracy: >90% reduction in cross-species contamination
- Marker gene specificity: Consistent improvement in fold-change ratios

## Performance Considerations

- **Memory usage**: Sparse matrices used throughout to minimize memory footprint
- **Clustering improves results**: Always provide cluster information when possible
- **Method selection**: Use "subtraction" for speed, "multinomial" for accuracy
- **Large datasets**: Consider using `method="soupOnly"` for >100k cells

## Troubleshooting

### Common Issues

**Low marker gene detection:**
```python
# Reduce stringency for marker detection
sc = soupx.autoEstCont(sc, tfidfMin=0.5, soupQuantile=0.8)
```

**High contamination estimates (>50%):**
```python
# Force acceptance of high contamination or manually set
sc.set_contamination_fraction(0.20, forceAccept=True)
```

**No clustering information:**
```python
# SoupX works without clustering but results are less accurate
corrected = soupx.adjustCounts(sc, clusters=False)
```

## Comparison with Other Methods

| Method | Speed | Accuracy | Requires Empty Droplets | Requires Clustering |
|--------|-------|----------|------------------------|-------------------|
| SoupX | Fast | High | Yes | Recommended |
| CellBender | Slow | High | No | No |
| DecontX | Medium | Medium | No | Yes |

## Contributing

We welcome contributions! Please see our [Contributing Guidelines](CONTRIBUTING.md) for details.

### Development Setup

```bash
git clone https://github.com/NiRuff/soupx-python.git
cd soupx-python
pip install -e ".[dev]"
pytest tests/
```

## License

This project is licensed under the GNU General Public License v2.0 - see the [LICENSE](LICENSE) file for details.

## Changelog

### v0.3.0 (Current)
- Full R compatibility 
- Automated contamination estimation
- Integration with scanpy ecosystem
- Comprehensive validation suite

### v0.2.0
- Core correction algorithms
- Manual contamination setting
- Basic 10X data loading

### v0.1.0
- Initial implementation
- Basic SoupChannel functionality

## Support

- **Issues**: [GitHub Issues](https://github.com/NiRuff/soupx-python/issues)
- **Questions**: [GitHub Discussions](https://github.com/NiRuff/soupx-python/discussions)
- **Citation**: Please cite the original SoupX paper (Young & Behjati, 2020)

## Acknowledgments

- Original SoupX developers: Matthew D. Young and Sam Behjati
- R package maintainers and contributors
- Python single-cell community (scanpy, anndata developers)

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