Welcome to OMICS integrator!

This application integrates different OMICS analysis applications.

File manager

Upload your analysis files.

Run analysis

Analysis type

Select the type of analysis type to do: VolcanoPlot, PCA, etc, and select the analysis application to use.

Input data

Provide the data for your analysis application.

Run analysis

Execute the analysis application selected. For a type of analysis several applications can be available.

Uploaded files

File preview

Select an application

For the selected analysis type the following applications are available.

Help

OMICS Integrator

This application allows to upload the files from an omic data study and run different omic data analysis applications.

OMICS integrator

The application menu is divided in the following options:

  • Home: introduction page of the application.
  • File manager: allows to upload the files from an omic data study.
  • Run analysis: allows to select the omic data analysis application, providing the files required by the application and execute it.
  • Help: application manual.
  • Terms & Conditions: terms & conditions of usage for the application.
  • About Us: details about the VHIR team.

File manager

To run the omic data analysis applications, the user must provide the files from the omic data study. These files can be uploaded in the File Manager option. The file manager is divided into 3 sections:

  • On the left side, it allows you to select a file, configure the options and add it to the file manager.
  • On the right side, the Uploaded files section shows the files available in the file manager.
  • On the right side, the File preview section shows a preview of the data of the last uploaded file.

File manager

Add a file

To add a file to the file manager:

  • Select the CSV file from the directory where it is stored on the computer.

  • Configure the file options:

    • Header: indicates if the first line of the file corresponds to the header with the names of the fields.
    • Separator: field separator.
    • Decimal separator: decimal separator for numeric data.

    The File preview panel shows a preview of the file data using the configured options.

  • Define the file type: TopTable, expression array, etc.

File manager - add a file

  • Click the Add file button. In the Uploaded files panel the added file is displayed.

File manager - file list

Remove a file

To delete a file from the file manager, press the Delete button displayed for the corresponding file.

Run analysis

After uploading the study files to the application as described in the previous section, this option allows to the user to select the analysis application and the required data required to run the analysis.

In the Analysis type panel, select the type of analysis to be performed in the Select the type of analysis field. When selecting an analysis type, a description of the analysis type is displayed next to the previous field, and at the bottom the applications that have been integrated into the system to perform this type of analysis. For example, in the following image we can see that when selecting the VolcanoPlot type of analysis, there are 2 applications: VolcanoPlot and VolcanoPlot 2.

Analysis applications available for VolcanoPlot analysis type

Moving the mouse over the applications displays a panel with additional information about the application and a button to select it.

Select an analysis application

Once an application is selected, a selection icon is displayed next to the name to identify it.

Selected analysis application

After selecting the application to use, the Input data panel shows the files that the application requires, allowing you to select them from the file manager. For example, for the selected application VolcanoPlot, a single file of type TopTable is required. The field shows all the files of this type available in the file manager.

Select analysis application files

Once the files required for the analysis have been selected, with the Run analysis button the analysis application can be launched. In the following image we can see the Volcano application using the data file selected in OMICS integrator.

VolcanoPlot application

Terms of Use

This application is hosted on a Shinyapps.io server https://www.shinyapps.io/.

By using this app you are agreeing to the terms of use as described by Shinnyaps.io: https://www.rstudio.com/about/shinyapps-terms-use/

We will not save your data on our servers. However, as the Shinyapps server is not HIPAA compliant, you must refrain from uploading protected health information or confidential data with this app. We are not responsible for the confidentiality, availability, security, loss, misuse or misappropriation of any data you submit to this application.

From the Shinyapps terms of use:

“If you choose to upload data to an application you are using via the RStudio Service, you acknowledge and agree you are giving certain legal rights to the licensor of the application to process and otherwise use your data. Please carefully review any license terms accompanying any application to which you submit your data for the legal rights which you are giving the application licensor. Further, RStudio does not claim ownership of your data; however, you hereby grant RStudio a worldwide, perpetual, irrevocable, royalty-free, fully paid up, transferable and non-exclusive license, as applicable, to use and copy your data in connection with making your data available to the application (and the licensor of such application) to which you have submitted your data. You acknowledge and agree that even if you remove your data from the RStudio Service, your data may have been downloaded by, and remain accessible to, the licensors of those applications to which you submitted your data. Accordingly, do not submit data which you desire to remain confidential or which you wish to limit the right to access or use. You should never submit to the RStudio Service any data which consists of personally identifiable information, credit card information, or protected health information, as such terms are defined by relevant laws, rules, and regulations. RSTUDIO IS NOT RESPONSIBLE FOR THE CONFIDENTIALITY, AVAILABILITY, SECURITY, LOSS, MISUSE OR MISAPPROPRIATION OF ANY DATA YOU SUBMIT TO THE RSTUDIO SERVICE OR ANY APPLICATION MADE AVAILABLE VIA THE RSTUDIO SERVICE.”

About Us

Creators of OMICS Integrator: Àlex Sánchez Pla and Jose Benito García Segura.

Àlex Sánchez Pla

PhD in Bioinformatics

Statistics and Bioinformatics Research Group (Vall d'Hebron Research Institute)

e-mail: alex.sanchez@vhir.org

Research areas:

Statistical analysis

Software development

Jose Benito García Segura

University Master's degree in Bioinformatics and Biostatistics (UOC, UB)

e-mail: jgarciasegu@uoc.edu