freeCount Bioinformatics Analysis Apps on Posit Cloud | R bloggers

Overview

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

free phone

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

The various analysis tools currently available include:

• Differential expression (DE) analysis – AND
• Network Analysis – THAT
• Functional analysis – FA
• Set up operations – SO

Set cloud

Set cloud allows you to do, share, teach and learn data science using RStudio or Jupyter Notebooks directly from your browser. Posit Cloud offers a personal workspace that allows you to work on your own content and have your content viewed by others.

Steps

The following steps will show you how to use the freeCount apps online with Posit Cloud.

1. Navigate to https://posit.cloud/ and log in (create an account if necessary)
2. In your workspace, click on “New Project” and select “New Project from Git Repository”
3. In the New Project from Git Repository pop-up window, type the following in the URL text box and click “OK”: https://github.com/ElizabethBrooks/freeCount To wait so the project can be deployed to your Posit Cloud workspace

4. Navigate to the “apps” folder in the file window (bottom right window)
5. Then navigate to the “cloud” folder in the file window
6. Select the application you want to run from the list of R shiny app files
7. Click the ‘Run App’ button in the top right corner of the source panel
8. Click “Yes” on the Install Shiny Package pop-up windowTo wait for the necessary R packages to install in your Posit Cloud workspace

   Finished! 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 pop-up window, type the following in the URL text box and click “OK”: https://github.com/ElizabethBrooks/freeCount

To wait…

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

Step 4

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

Step 5

Then navigate to the “cloud” folder in the file window.

Step 6

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

Step 7

Click the ‘Run App’ button in the top right corner of the source panel.

Step 8

Click “Yes” on the Install Shiny Package pop-up window.

To wait…

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

Finished!

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 the delete tabs feature in Chrome. Chrome automatically removes background tabs to save memory.

Important note

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

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