Overview

One way that you can use the freeCount R Shiny applications (apps) online is through Posit Cloud, which lets you access powerful data science tools in your browser without the need for installation or complex configuration.

freeCount

The freeCount analysis framework provides a modular set of tools and tutorials for a structured approach to biological count data analysis. Users are guided through common data assessment, processing and analysis approaches.

The different analysis tools currently available include:

• Differential Expression (DE) Analysis – DA
• Network Analysis – NA
• Functional Analysis – FA
• Set Operations – SO

Posit Cloud

Posit Cloud enables you to do, share, teach and learn data science using RStudio or Jupyter Notebooks directly from your browser. Posit Cloud provides a personal workspace that allows you to work on your own content, and you can let your content be viewed by others.

Steps

The following steps will walk you through how to run the freeCount apps online using Posit Cloud.

1. Navigate to https://posit.cloud/ and log in (create an account, if necessary)
2. In your workspace, click “New Project” and select “New Project from Git Repository”
3. In the New Project from Git Repository popup window, enter the following in the URL text box and click “OK”: https://github.com/ElizabethBrooks/freeCount 
   
   Wait for the project to deploy in your Posit Cloud workspace 
   
   
4. Navigate to the “apps” directory in the file pane (bottom right window)
5. Next, navigate to the “cloud” directory in the file pane
6. Select the application that you want to run from the list of R shiny app files 
7. Click the “Run App” button in the upper right corner of the source pane
8. Click “Yes” on the Install Shiny Package popup window
   
   Wait for the necessary R packages to install in your Posit Cloud workspace
   
   Done! Finally, the shiny app should launch and allow you to run the selected analysis

---

Step 1

Navigate to https://posit.cloud/ and log in (create an account, if necessary).

Step 2

In your workspace, click “New Project” and select “New Project from Git Repository”.

Step 3

In the New Project from Git Repository popup window, enter the following in the URL text box and click “OK”: https://github.com/ElizabethBrooks/freeCount 

Wait…

Wait for the project to deploy in your Posit Cloud workspace.

Step 4

Navigate to the “apps” directory in the file pane (bottom right window).

Step 5

Next, navigate to the “cloud” directory in the file pane.

Step 6

Select the application that you want to run from the list of R shiny app files.

Step 7

Click the “Run App” button in the upper right corner of the source pane.

Step 8

Click “Yes” on the Install Shiny Package popup window.

Wait…

Wait for the necessary R packages to install in your Posit Cloud workspace.

Done!

Finally, the shiny app should launch and allow you to run the selected analysis.

---

Troubleshooting

Posit Cloud R session disconnected – If you are using Google Chrome, try disabling Chrome’s tab discarding feature. Chrome automatically unloads background tabs to save memory.

---

Important Note

Note that not all of the apps or features are available for the cloud version of the freeCount apps due to the limits on the free plan for Posit Cloud.