Structurexplor

A plateform (Shiny App)for the exploration of structural features of RNA secondary structures.

Discovering function-related structural features, such as the cloverleaf shape of transfer RNA secondary structures, is essential to understand RNA function. With this aim, we have developed a platform, named Structurexplor, to facilitate the exploration of structural features in populations of RNA secondary structures. It has been designed and developed to help biologists interactively search for, evaluate and select interesting structural features that can potentially explain RNA functions.

Exploring your RNA secondary structures

Go to Structurexplor web application based on Shiny and start exploring your RNA secondary structures.

Structurexplor web app. has been successfully tested on modern browsers: Firefox 50, Chrome 55 and Safari 10.

How to run Structurexplor on a local machine or deploy on a local server (Ubuntu 16.04)

1. Download and install the latest version of R (>=3.2.3) for Ubuntu 16.04 also called Ubuntu Xenial Xerus.

2. Download and unzip the Structurexplor repository

3. Start R command line by opening the terminal and by typing 'R'.

4. At the R prompt, install and load the following packages using the following commands install.packages("devtools"); require(devtools); install_github("ramnathv/rCharts"); require(rCharts); source("https://bioconductor.org/biocLite.R"); biocLite(c("BiocGenerics", "Biostrings")); require(BiocGenerics); require(Biostrings); packList=c('shiny','rmarkdown','shinydashboard','ape','rjson','jsonlite','pvclust','colorspace','DT','cluster','plyr','shinyjs','shinyBS'); lapply(packList, install.packages, character.only = TRUE); lapply(packList, require, character.only = TRUE) Note that devtools required 'libcurl4-openssl-dev' to be installed via ubuntu terminal by the following command: sudo apt-get install libcurl4-openssl-dev

Supplementary step to run Structurexplor on a local machine

• Start Structurexplor using shiny::runApp("path_to_Structurxplor")

Supplementary steps to run Structurexplor on a local server

The middleware open source ShinyProxy has been used to deploy Structurexplor.

• To install and configure ShinyProxy please follow the detailed procedure in the Getting started menu.

• The instructions to deploy a local instance of Shinyproxy is provided in the Deploying Apps menu.

Post suggestions or issues

Please report suggestions or issues here.

How to cite Structurexplor

Glouzon, J-PS, Perreault J-P, Wang S. Structurexplor:An interactive plateform to explore structural features of RNA secondary structures. Bioinformatics. 2017.

Licence

Structurexplor is released under the terms of the GNU GPL licence. For further informations, please see the LICENCE file of the repository.