RNAFramework

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RNA structure probing and post-transcriptional modifications mapping high-throughput data analysis

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![RNAFramework logo](https://www.incarnatolab.com/images/software/rnaframework.png)

## Introduction

The recent advent of Next Generation Sequencing (NGS) techniques, has enabled transcriptome-scale analysis of the RNA epistructurome.
Despite the establishment of several methods for querying RNA secondary structures (CIRS-seq, SHAPE-seq, Structure-seq, DMS-seq, PARS, SHAPE-MaP, DMS-MaPseq), and RNA post-transcriptional modifications (&Psi;, m1A, m6A, m5C, hm5C, 2'-OMe) on a transcriptome-wide scale, no tool has been developed to date to enable the rapid analysis and interpretation of this data.

__RNA Framework__ is a modular toolkit developed to deal with RNA structure probing and post-transcriptional modifications mapping high-throughput data.  
Its main features are:

- Automatic reference transcriptome creation
- Automatic reads preprocessing (adapter clipping and trimming) and mapping
- Scoring and data normalization
- Accurate RNA folding prediction by incorporating structural probing data

For updates, please visit: <http://www.rnaframework.com>

For support requests, please post your questions/issues to: <https://github.com/dincarnato/RNAFramework/issues>

## Author

Danny Incarnato (dincarnato[at]rnaframework.com)  
University of Groningen

## References

Incarnato *et al.*, 2018. RNA Framework: an all-in-one toolkit for the analysis of RNA structures and post-transcriptional modifications. *Nucleic Acids Research* [PMID: [29893890](https://pubmed.ncbi.nlm.nih.gov/29893890/)]

## License

This program is free software, and can be redistribute and/or modified under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or any later version.

Please see <http://www.gnu.org/licenses/> for more information.

## Documentation

For any information, please refer to the documentation: <http://rnaframework-docs.readthedocs.io/>

RNAFramework

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