Prerequisites
==============
Before launching the AGNE application, ensure all necessary packages are installed. To simplify this process, a script named `Needed_packages.R` is provided.

**Steps to Install Required Packages:**

1. Open R or RStudio.
2. Run the following command to execute the `Needed_packages.R` script:

   .. code-block:: R

      source("Needed_packages.R")

   This will automatically install and load all the required packages for the application.

3. Ensure all installations are successful. If any errors occur, check your internet connection and verify R is configured to install packages.

**File Details:**
- **`Needed_packages.R`**: Installs and loads all necessary R packages.
- **`AGNE_app.R`**: The main application script.

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Launching the Application
--------------------------
Once all packages are installed, you can launch the application:

1. Open R or RStudio.
2. Set the working directory to the location of the `AGNE_app.R` file:

.. code-block:: R

    setwd("/path/to/your/app")

3. Run the application using the following command:


.. code-block:: R

    shiny::runApp("AGNE_app.R")

The application will start running in your default web browser.

**Optional Features:**

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Important Notes
---------------
- Always run `Needed_packages.R` first to ensure all dependencies are installed.
- If new packages are required for additional features, re-run the script to update your environment.
- The AGNE application requires an active internet connection to install packages and access external resources such as the Gene Ontology and KEGG databases.