EMImR: a Shiny Application for Identifying Transcriptomic and Epigenomic Changes

Table of Contents

1. About EMImR
2. Demonstration Video
3. Implementation and Operation
4. Installation Guides
5. Resource consumption
6. Licence
7. Citation

About EMImR

EMImR is a Shiny Application for Transcriptomic and Epigenomic Changes Identification and data correlation.

The application's main function is to identify the intersection between genetic and epigenetic modififcations, including :

• Identify the differentially expressed genes (DEGs)

• Identify the differentially methylated genes (DMGs)

• Determine DEGs associated with DMGs

• Identify the genes associated to differentially expressed interfering miRNA (GDEImRs).

• Determine DEGs associated with differentially expressed interfering miRNA

Demonstration Video

Implementation and Operation

- platform-independent
- all dependencies are installed automatically with the tool
- Internet requirement: Only if using an online server
- Third-party tools requirement: R studio or an online Server
- Pre-requirements: R  installation

Installation Guide

Step 1 : Install dependencies

Install the latest version of R if your computer does not have it: [R](https://cran.r-project.org/bin/windows/base/)   

        ### How To Install R and RStudio
        - Go to This Website : https://posit.co/download/rstudio-desktop/

        -  Download R for you specific Operating System (OS). R 4.2.1 version is recommended [Link to version 4.2.1](https://cran.r-project.org/bin/windows/base/old/4.2.1/)

       - Download RStudio

Step 2 : Download the application

Download the application folder   

Step 3 : Open the application

- Open the application folder using RStudio   

- Set the folder as a working directory

- Then open the file named "Run_App.R"

Step 4 : Run The Application

Run the app code by cicking on the "Run APP" button

All dependencies will be installed automaticly and the application's dashboard will appear.

Resource consumption

The Shiny application was executed on a Lenovo PC equipped with an Intel® Core™ i5-10210U CPU @ 1.60 GHz, 36 GB of RAM, running a 64-bit Windows 10 operating system. During execution, the application consumed approximately 2.5 GB of memory, utilized up to 24% of CPU, and 1% of GPU resources, as observed in Windows Task Manager.

Licence

The scripts are under the artistic-2.0 license, and the CSV data are under the CC0 public domain waiver.

Citation

Ben Aribi, H., Ayadi, F., Naitore, C., Guerbouj, S. & Awe, O. I. (2024). EMImR: a Shiny Application for Identifying Transcriptomic and Epigenomic Changes. Zenodo. https://doi.org/10.5281/zenodo.16881955

Note

Tool Developer / Maintainer: Hiba Ben Aribi

Email: [email protected]