Question 1

What is SCenic Viewer?

Accepted Answer

SCenic Viewer is a tool used to visualize your single-cell data, hence the SC in the name. It is a web-based application that allows users to make quick decisions about their experimental data, which is contained in the RDS (Seurat) object. For example, if your trusted bioinformatician has helped you generate an RDS object, you can use SCenic Viewer to quickly determine if your data is represented properly based on how it is visualized in UMAP, Violin, and Feature plots.

Question 2

What is the maximum size of the RDS object that can be loaded into SCenic Viewer?

Accepted Answer

The maximum size of the RDS object that can be uploaded into SCenic Viewer is 17 GB.

Question 3

Who is the ideal user for SCenic Viewer?

Accepted Answer

Bench scientists and researchers, specifically molecular and cellular biologists, who are interested in evaluating gene expression patterns with single-cell resolution would most benefit from using SCenic Viewer.

Question 4

How do I access SCenic Viewer?

Accepted Answer

You can access SCenic Viewer using the Bridge Horizon dashboard by navigating to the left-hand sidebar and clicking on the "Apps" section. Once there you will find applications that are under subscription. Initialize SCenic Viewer by clicking on the "Launch" button.

Question 5

Which browser does SCenic Viewer work best on?

Accepted Answer

SCenic Viewer works well on Firefox, Chrome, Safari, and Opera browsers.

Question 6

Can I access SCenic Viewer on a mobile device?

Accepted Answer

Yes. You can open SCenic Viewer using the appropriate web browser on your mobile device. SCenic Viewer has been visualized on both Android and Apple operating systems. To access SCenic Viewer, open your preferred browser, log in to the Bridge Horizon dashboard, navigate to the "Apps" section in the left-hand sidebar, and click the "Launch" button.

Question 7

How do I upload data to SCenic Viewer?

Accepted Answer

SCenic Viewer does not have data storage capabilities. You must first upload data on Bridge Horizon, then that data will be available in SCenic Viewer. Please exit the SCenic Viewer application and return to the Bridge Horizon dashboard homepage to upload data.

Question 8

How do I access the data I uploaded to Bridge Horizon?

Accepted Answer

Once logged into Bridge Horizon, navigate to the left-hand sidebar and click on the "Data" tab. This opens the "My Data" and "Trash" menus. All uploaded data will be in the "My Data" menu item. Please note that any item placed in the "Trash" menu will be deleted within 30 days.

Question 9

Should my data include annotations?

Accepted Answer

No, your data doesn't need to be annotated. By default, during cell clustering and community detection, Seurat automatically attaches cluster numbers to each population of cells. These clusters can still be visualized using SCenic Viewer.

Question 10

What if my data does not include annotations?

Accepted Answer

If your data does not include annotations, clusters will be labeled with Seurat-assigned cluster numbers. The UMAP, violin, and feature plots will simply show profiles based on cell cluster numbers. In this scenario, you can perform marker gene analysis using SCenic Viewer to find the appropriate labels for your cell clusters.

Question 11

My data is bigger than 15 GB. How do I modify the file so it fits with SCenic Viewer?

Accepted Answer

Currently SCenic Viewer does not support RDS objects larger than 17 GB in size. In addition, the RDS object must contain single-cell RNA-seq or CITE-seq data that has been processed via the Seurat pipeline; SCenic Viewer is not compatible with other analysis pipelines (such as Scanpy or Monocle). If your object is larger than 15 GB, reduce the size of your RDS object by subsampling cells from within each Seurat cluster or annotated cell population until the object is below 17 GB. Please consult a trained bioinformatician or data scientist to perform this task.

Question 12

How do I generate a UMAP?

Accepted Answer

Navigate to the "Apps" section on Bridge Horizon and launch SCenic Viewer by clicking the "Launch" button. Once inside SCenic Viewer, click the "Browse" button under the "Choose a File" section to open the file browser. Note that only RDS objects will be available for viewing. Select your RDS object, and once loaded, SCenic Viewer will automatically populate the UMAP plot. For more detailed instructions, refer to the SCenic Viewer tutorial.

Question 13

How do I generate a violin plot?

Accepted Answer

Once you have loaded an RDS object, navigate to the "Violin Plot" tab and enter your genes of interest in the "Genes" text box. SCenic Viewer will search for the genes you entered in your RDS object, and if a gene name is not found, it will automatically search for gene aliases. For instance, if you entered p15ink4b and it is not detected, SCenic Viewer will search for the associated aliases Cdkn2b and Tp15. If the gene or its aliases are found, a violin plot will be generated, one plot per gene, with expression profiles for each cluster separated along the x-axis.

Question 14

How do I generate a feature plot?

Accepted Answer

Once you have loaded an RDS object, navigate to the "Feature Plot" tab and enter your genes of interest in the "Genes" text box. SCenic Viewer will search for the genes, and if a gene name is not found, it will automatically search for gene aliases. If the gene or its alias is detected in the RDS object, a feature plot will be generated in the plot canvas, one plot per gene.

Question 15

How do I modify the font in my plot?

Accepted Answer

Navigate to the "Label" menu in the right sidebar in SCenic Viewer. Note that the right sidebar may be pushed below the plot canvas depending on the size of your browser window and the resizing of the plot. Once in the "Label" menu, the font size of the main title or the x- and y-axis labels can be altered with values entered in the "Size" text box. You can also bold or italicize fonts using the radio buttons under "Style".

Question 16

How do I modify the axis titles in my plot?

Accepted Answer

Navigate to the "Label" menu in the right sidebar in SCenic Viewer. Axis titles can be altered via the text boxes under the "X-axis Label" and "Y-axis Label" sections.

Question 17

How do I modify the colors of figures in my plot?

Accepted Answer

Only the UMAP plot can be configured to a different color palette. Navigate to the "Colors" menu in the right sidebar (it may be pushed below the plot canvas depending on your browser window size) and click the dropdown under "Choose a Color Palette" to access the available color palettes.

Question 18

How do I resize a plot for easier interpretation?

Accepted Answer

Each plot canvas in SCenic Viewer has a small triangle at the bottom right-hand corner. Click and hold the small triangle, then drag to resize the plot canvas.

Question 19

I'd like to download an image of my plot. What formats can I choose from?

Accepted Answer

You can download high-resolution images in various formats including PNG, PDF, and JPG.

Question 20

How do I download an image of my plot?

Accepted Answer

Click the blue download button above the plot canvas, beside the "File Name" section in SCenic Viewer. The name of the file can be changed via the text box under the "File Name" section; by default the file name placeholder is "example_filename".

Question 21

What can I do if I have questions that are not answered in this FAQ?

Accepted Answer

If you have a question that is not addressed in the FAQ, please contact us at support@bridgeinformatics.com.

SCenic Viewer: Frequently Asked Questions

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