Metadata-Version: 2.4
Name: ribotools
Version: 2.0.0
Summary: Ribotools: a toolbox for translation efficiency (TE) and differential expression (DE) analyses
Author: Etienne Boileau
Maintainer-email: Etienne Boileau <boileau@uni-heidelberg.de>
License-Expression: MIT
Project-URL: Github, https://github.com/eboileau/ribotools/
Project-URL: Issues, https://github.com/eboileau/ribotools/issues
Keywords: Bioinformatics,Ribo-seq/Ribosome profiling,RNA-seq/RNA sequencing,Translation efficiency (TE),Differential expression (DE)
Classifier: Development Status :: 5 - Production/Stable
Classifier: Intended Audience :: Science/Research
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Operating System :: MacOS :: MacOS X
Classifier: Operating System :: POSIX :: Linux
Classifier: Programming Language :: Python :: 3.11
Classifier: Programming Language :: Python :: 3.12
Classifier: Programming Language :: Python :: 3.13
Requires-Python: <3.14,>=3.11
Description-Content-Type: text/markdown
License-File: LICENSE
Requires-Dist: rpbp>=4.0.1
Requires-Dist: htseq
Provides-Extra: tests
Requires-Dist: pytest; extra == "tests"
Requires-Dist: pytest-cov; extra == "tests"
Requires-Dist: pytest-depends; extra == "tests"
Provides-Extra: docs
Requires-Dist: ipykernel; extra == "docs"
Requires-Dist: matplotlib; extra == "docs"
Requires-Dist: nbsphinx; extra == "docs"
Requires-Dist: pandoc; extra == "docs"
Requires-Dist: sphinx; extra == "docs"
Requires-Dist: sphinx_rtd_theme; extra == "docs"
Requires-Dist: furo; extra == "docs"
Requires-Dist: sphinx-argparse; extra == "docs"
Requires-Dist: sphinx-copybutton; extra == "docs"
Dynamic: license-file

# Ribotools

**Ribotools**, an _add-on_ to [Rp-Bp](http://rp-bp.readthedocs.io/en/latest/), is a toolbox for the analysis of matched ribosome profiling (Ribo-seq) and RNA sequencing (RNA-seq) data.

**Ribotools** can be used to generate count tables, starting from raw, trimmed reads, or existing alignments, taking into consideration Ribo-seq periodicity estimates and RNA-seq fragment length. **Ribotools** can perform translation efficiency (TE) or differential expression (DE) analysis, using standard features such as genes (exon or CDS), or Ribo-seq ORFs, accommodating for sample-to-sample variance, complex experimental designs, or confounding factors. For TE analysis, features are automatically classified into different regulatory layers.

<p align="center">
  <a href="https://ribotools.readthedocs.io/en/latest"><img alt="Ribotools" src="https://github.com/eboileau/ribotools/raw/master/docs/source/_static/ribotools-logo-light.png"></a>
</p>

<p align="center">
<a href="http://bioconda.github.io/recipes/ribotools/README.html"><img alt="Install with bioconda" src="https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat"></a>
<a href="https://pypi.org/project/ribotools/"><img alt="PyPI" src="https://img.shields.io/pypi/v/ribotools"></a>
<a href="https://github.com/eboileau/ribotools/actions/workflows/ci.yml"><img alt="CI" src="https://github.com/eboileau/ribotools/actions/workflows/ci.yml/badge.svg"></a>
<a href='https://ribotools.readthedocs.io/en/latest/?badge=latest'>
    <img src='https://readthedocs.org/projects/ribotools/badge/?version=latest' alt='Documentation Status' />
</a>
</p>

---

## Documentation

Consult the [user guide](https://ribotools.readthedocs.io/en/latest) for instructions on how to install the package and detailed usage instructions.

## How to report issues

For bugs, issues, or feature requests, use the [bug tracker](https://github.com/eboileau/ribotools/issues). Follow the instructions and guidelines given in the templates.

## License

The MIT License (MIT). Copyright (c) 2019 Etienne Boileau.
