semvec/pypi-packages huggingface dataset:
deseq2-go-pipeline 0.3.0
Python wrapper for DESeq2 and GO enrichment analysis using R
License: MIT
Requires Python: >=3.8
Keywords: bioinformatics, deseq2, gene-expression, go-enrichment, rpy2

# DESeq2 GO Pipeline

A Python wrapper for R-based differential expression analysis using DESeq2 and Gene Ontology enrichment analysis.

## Installation

### Prerequisites

This package requires R (version 4.0 or higher) and several Bioconductor packages. Install them in R:

```r
if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install(c("DESeq2", "clusterProfiler", "org.At.tair.db", "AnnotationDbi"))
```

### Python Package Installation

```bash
pip install deseq2-go-pipeline
```

## Quick Start

```python
from deseq2_go_pipeline import DESeq2GOPipeline
import pandas as pd

# Initialize pipeline
pipeline = DESeq2GOPipeline()

# Load your data
counts_df = pd.read_excel('normalized_count.xlsx')
metadata_df = pd.read_excel('DEseq2_metadata.xlsx')

# Run analysis
dds = pipeline.make_dds(counts_df, metadata_df)
de_results = pipeline.compare_filter_annot(
    dds=dds,
    group_test='treatment',
    group_base='control',
    write_excel=True,
    output_dir='./results'
)
```

## Features

- Seamless integration between Python and R for bioinformatics workflows
- Adjustable filtering criteria for differential expression analysis
- Automated GO enrichment analysis with custom metrics
- Excel output for easy data sharing
- Robust error handling and logging

## Requirements

- Python >= 3.8
- R >= 4.0
- rpy2 >= 3.5.0
- pandas >= 1.3.0
- openpyxl >= 3.0.0

## License

MIT License - see LICENSE file for details.

## Citation

If you use this package in your research, please cite:
[Your publication information here]

## Support

For issues and feature requests, please use the [GitHub issue tracker](https://github.com/yourusername/deseq2-go-pipeline/issues).