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### Regeneration Rosetta: An interactive web application to explore regeneration-associated gene expression and chromatin accessibility
Andrea Rau, Sumona Dhara, Ava Udvadia, Paul Auer
[](https://zenodo.org/badge/latestdoi/184636910)
<img src="rosetta.png" align="right" />
Time-course high-throughput assays of gene expression and enhancer usage in zebrafish provide a valuable characterization of the dynamic mechanisms governing gene regulatory programs during CNS axon regeneration. To facilitate the exploration and functional interpretation of a set of fully-processed data on regeneration-associated temporal transcription networks, we have created an interactive web application called [*Regeneration Rosetta*](http://ls-shiny-prod.uwm.edu/rosetta/). Using either built-in or user-provided lists of genes in one of dozens of supported organisms, our web application facilitates the (1) visualization of clustered temporal expression trends; (2) identification of proximal and distal regions of accessible chromatin to expedite downstream motif analysis; and (3) description of enriched functional gene ontology categories. By enabling a straightforward interrogation of these rich data without extensive bioinformatic expertise, Regeneration Rosetta is broadly useful for both a deep investigation of time-dependent regulation during regeneration in zebrafish and hypothesis generation in other organisms.
This repository contains the following source code files used to create the *Regeneration Rosetta* R/Shiny app. It is organized as follows:
- `index.Rmd`: primary file for *Regeneration Rosetta* app
- `OpticRegen_format.R`: helper file to organize and prepare data outside of the app to improve run time
- `restart.txt`: empty file whose last modified date/time triggers a new deployment on the Shiny server
- `data/`: folder containing all necessary data files for the app to run (essentially .rds files + one Excel file and one SQLite database)
- `images/`: folder containing logos and images
- `misc/`: folder containing a helper script to output data for the 7480 significantly DE transcripts used in the app.
This resource is available under the [GNU public license](https://www.gnu.org/licenses/gpl-3.0.en.html) (GPL-3). If you use any of the results or figures generated by this app in a publication or presentation, please cite our work:
* Rau et al. (2019) Regeneration Rosetta: An interactive web application to explore regeneration-associated gene expression and chromatin accessibility. *G3: Genes|Genomes|Genetics* 9(12):3953-3959. https://doi.org/10.1534/g3.119.400729.
* Dhara et al. (2019) Regulation of CNS regeneration-associated genes is driven by a temporally changing cast of transcription factors. *Scientific Reports* 9:14198. https://doi.org/10.1038/s41598-019-50485-6.
* [Regeneration Rosetta](http://ls-shiny-prod.uwm.edu/rosetta): doi: https://doi.org/10.5281/zenodo.2658771.
* Source code for Dhara et al. (2019): https://zenodo.org/badge/latestdoi/184628135.
* Source code for the Regeneration Rosetta: https://zenodo.org/badge/latestdoi/184636910