Metadata-Version: 2.4
Name: RiboParser
Version: 0.2.7.8
Summary: A pipeline for ribosome profiling data analysis
Author-email: Ren Shuchao <rensc0718@163.com>
License-Expression: GPL-3.0-or-later
Project-URL: Homepage, https://github.com/renscq/RiboParser
Classifier: Programming Language :: Python :: 3.12
Classifier: Operating System :: POSIX :: Linux
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Intended Audience :: Science/Research
Requires-Python: >=3.12
Description-Content-Type: text/markdown
Requires-Dist: numpy>=1.26
Requires-Dist: pandas>=2.2
Requires-Dist: pyarrow>=15
Requires-Dist: polars>=1.0
Requires-Dist: biopython>=1.83
Requires-Dist: scipy>=1.12
Requires-Dist: scikit-learn>=1.4
Requires-Dist: statsmodels>=0.14
Requires-Dist: pysam>=0.23
Requires-Dist: joblib>=1.3
Requires-Dist: matplotlib>=3.8
Requires-Dist: matplotlib-venn>=1.1
Requires-Dist: seaborn>=0.13

# RiboParser

<p align="center">
  <strong>RiboParser</strong> is a modular command-line toolkit for comprehensive RNA-seq and Ribo-seq data analysis.
</p>

<p align="center">
  📖 <a href="https://renscq.github.io/RiboParser/">Documentation</a> |
  🐞 <a href="https://github.com/Renscq/RiboParser/issues">Issues</a> |
  📚 <a href="#citation">Citation</a> |
  📝 <a href="#license">License</a>
</p>

---

## Overview

RiboParser provides an integrated workflow for RNA-seq and ribosome profiling (Ribo-seq) analysis, including reference preparation, raw data preprocessing, alignment, quantification, quality control, RPF density construction, gene-level analysis, codon-level analysis, SeRP analysis, smORF analysis, and downstream visualization with RiboShiny.

The full documentation is available at:

<https://renscq.github.io/RiboParser/>

## Installation

```bash
conda install riboparser -c rensc
# or
micromamba install riboparser -c rensc
```

```bash
pip install riboparser
```

## Quick test

```bash
riboparser -v
riboparser -c
riboparser -d
riboparser -m
```

## Citation

Ren, S., Li, Y. & Zhou, Z.  
**RiboParser/RiboShiny: An integrated platform for comprehensive analysis and visualization of ribo-seq data.**  
*Journal of Genetics and Genomics* (2025).  
DOI: **10.1016/j.jgg.2025.04.010**

## License

GPL-3.0-or-later.
