Metadata-Version: 2.4
Name: rpbp
Version: 4.0.1
Summary: Rp-Bp: Ribosome Profiling with Bayesian Predictions
Author: Brandon Malone
Maintainer-email: Etienne Boileau <boileau@uni-heidelberg.de>
License-Expression: MIT
Project-URL: Github, https://github.com/dieterich-lab/rp-bp
Project-URL: Issues, https://github.com/dieterich-lab/rp-bp/issues
Keywords: Bioinformatics,Ribo-seq/Ribosome profiling quality control,Open reading frame (ORF) discovery,Translation prediction
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: pbiotools>=5.0.0
Requires-Dist: appdirs
Requires-Dist: cmdstanpy
Requires-Dist: dash
Requires-Dist: dash-bio
Requires-Dist: dash-bootstrap-components
Requires-Dist: pyyaml
Requires-Dist: statsmodels
Provides-Extra: tests
Requires-Dist: pytest; extra == "tests"
Requires-Dist: pytest-cov; extra == "tests"
Requires-Dist: pytest-depends; extra == "tests"
Provides-Extra: docs
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Requires-Dist: sphinx; extra == "docs"
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Requires-Dist: sphinx-argparse; extra == "docs"
Requires-Dist: sphinx-copybutton; extra == "docs"
Dynamic: license-file

# Ribosome profiling with Bayesian predictions (Rp-Bp)

Ribosome profiling (Ribo-seq) is an RNA-sequencing-based readout of RNA translation. Isolation and deep-sequencing of ribosome-protected RNA fragments (ribosome footprints) provides a genome-wide snapshot of the translatome at sub-codon resolution. **Rp-Bp** is an unsupervised Bayesian approach to predict translated open reading frames (ORFs) from ribosome profiles. **Rp-Bp** can be used for ORF discovery, or simply to estimate periodicity in a set of Ribo-seq samples. When used for ORF discovery, **Rp-Bp** automatically classifies ORFs into different biotypes or categories, relative to their host transcript.

**Rp-Bp** comes with two _interactive dashboards_ or _web applications_, one for read and periodicity quality control, the other to facilitate Ribo-seq ORFs discovery.

<p align="center">
  <a href="https://rp-bp.readthedocs.io/en/latest/"><img alt="Rp-Bp" src="https://github.com/dieterich-lab/rp-bp/raw/master/docs/source/_static/logo-rpbp-dark.png"></a>
</p>

<p align="center">
<a href="http://bioconda.github.io/recipes/rpbp/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/rpbp/"><img alt="PyPI" src="https://img.shields.io/pypi/v/rpbp"></a>
<a href="https://github.com/dieterich-lab/rp-bp/actions/workflows/ci.yml"><img alt="CI" src="https://github.com/dieterich-lab/rp-bp/actions/workflows/ci.yml/badge.svg"></a>
<a href="https://rp-bp.readthedocs.io/en/latest/?badge=latest"><img alt="Docs" src="https://readthedocs.org/projects/rp-bp/badge/?version=latest"></a>
</p>

---

## Documentation

Consult the [user guide](http://rp-bp.readthedocs.io/en/latest/) for instructions on how to install the package, or to use Docker/Singularity containers with the package pre-installed. Detailed usage instructions and tutorials are available.

## How to report issues

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

## How to cite

Brandon Malone, Ilian Atanassov, Florian Aeschimann, Xinping Li, Helge Großhans, Christoph Dieterich. [Bayesian prediction of RNA translation from ribosome profiling](https://doi.org/10.1093/nar/gkw1350), _Nucleic Acids Research_, Volume 45, Issue 6, 7 April 2017, Pages 2960-2972.

## License

The MIT License (MIT). Copyright (c) 2016 dieterich-lab.
