Metadata-Version: 2.1
Name: seismic-rna
Version: 0.9.5
Summary: RNA Structure Ensemble Inference via Sequencing, Mutation Identification, and Clustering
Project-URL: Homepage, https://github.com/rouskinlab/seismic-rna
Project-URL: Bug Tracker, https://github.com/rouskinlab/seismic-rna/issues
Author: Matty Allan, Yves Martin, Scott Grote, Alberic de Lajarte
License: GPL-3.0-only
License-File: LICENSE
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python :: 3
Requires-Python: >=3.10
Requires-Dist: brotli>=1.0
Requires-Dist: click>=8.1
Requires-Dist: cutadapt>=4.4
Requires-Dist: fastqsplitter>=1.2
Requires-Dist: matplotlib>=3.6
Requires-Dist: networkx>=3.1
Requires-Dist: numpy>=1.23
Requires-Dist: pandas>=1.5
Requires-Dist: plotly>=5.11
Requires-Dist: pyyaml>=6.0
Requires-Dist: scipy>=1.9
Requires-Dist: sphinx-click>=4.4
Requires-Dist: sphinx-panels>=0.6.0
Requires-Dist: sphinx-rtd-theme>=1.3.0
Requires-Dist: sphinx>=4.5
Requires-Dist: sphinxcontrib-blockdiag>=3.0.0
Description-Content-Type: text/markdown


# SEISMIC-RNA

RNA Structure Ensemble Inference by Sequencing, Mutation Identification,
and Clustering

![Logo of SEISMIC-RNA](logo/logo-1200.png "SEISMIC-RNA")


## About

SEISMIC-RNA analyzes data from RNA mutational profiling experiments,
such as [DMS-MaPseq](https://www.nature.com/articles/nmeth.4057)
and [SHAPE-MaP](https://www.nature.com/articles/nmeth.3029).
This software introduces an optimized implementation of the algorithm
[DREEM](https://www.nature.com/articles/s41586-020-2253-5) for detecting
and quantifying RNA structure ensembles.


## Installation and Usage

Documentation for installing and using SEISMIC-RNA is available on
[GitHub Pages](https://rouskinlab.github.io/seismic-rna).


## Issues

The [issue page](https://github.com/rouskinlab/seismic-rna/issues) of
the GitHub repository is the official location for reporting bugs and
other issues. Before opening a new issue, please check if a similar
issue already exists.


## Contributors

SEISMIC-RNA has been developed by the following individuals in the lab
of [Silvi Rouskin](https://rouskinlab.com) at Harvard Medical School:

- [Matthew "Matty" Allan](https://github.com/matthewfallan)
- [Yves Martin](https://github.com/yvesmartindestaillades)
- [Scott Grote](https://github.com/heWhosShouldersBlockTheSun)
- [Albéric de Lajarte](https://github.com/AlbericDeLajarte)
