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README.md

RNAFramework logo


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 (Ψ, 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
For news, and walkthrough examples, please visit our blog: http://www.rnaframework.com/blog

Author

Danny Incarnato (dincarnato[at]rnaframework.com)
Epigenetics Unit @ HuGeF [Human Genetics Foundation]

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.readthedocs.io/

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

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