Example dataset where tSNE, UMAP and PCA have been visualized

[Tulasi S]

Hello Team,

We actually found a paper (https://www.biorxiv.org/content/10.1101/2020.10.31.363580v1.full.pdf) about  OmicPioneer-sc an open-source data visualization/analysis package that integrates dimensionality-reduction plots (DRPs) such as t-SNE and UMAP with Next-Generation Clustered Heat Maps (NGCHMs) and Pathway Visualization Modules (PVMs) in a seamless, highly interactive exploratory environment. They have also stated that they have implemented plug-in status or links with a number of capable bioinformatic environments, including cBioPortal. So is there any example dataset where tSNE, UMAP and PCA plots are visualised? Can you please help us with the example dataset if there is any.

Thanks and regards,

Tulasi S

[Tulasi S]

Hello Team, 

This is a gentle reminder for the above mail. Is there any update regarding the same? Eager to hear from you.

Thanks & Regards,

Tulasi S

[Jessica Singh]

HI Tulasi, 

Apologies for the delayed response. I looked into the paper, and it seems like a great feature. However, this feature has not been implemented in the public cBioPortal portal, so we can't share any such examples with you (concerning the dimensionality-reduction plots). You can contact the authors and check if they implemented this plug-in on their local cBioPortal installation and get more information from them. 

Regarding the pathway feature, cBioPortal uses PathwayMapper, as shown in this example. This feature already exists in cBioPortal but doesn't use the open-source tool from the paper. 

We are working on adding more single-cell data into cBioPortal, which includes allowing users to visualize their dimensionality reduction plots. We allow users to do this using either cellxgene or VITESSCE - like in this example. I'd be happy to answer more questions about this.  

I hope this answers your question. 

Regards, 

Jessica

On Tue, Nov 22, 2022 at 9:58 AM Tulasi S <tula...@strandls.com> wrote:

Hello Team, 

This is a gentle reminder for the above mail. Is there any update regarding the same? Eager to hear from you.

Thanks & Regards,

Tulasi S

On Thu, Nov 10, 2022, 5:10 PM Tulasi S <tula...@strandls.com> wrote:

Hello Team,

We actually found a paper (https://www.biorxiv.org/content/10.1101/2020.10.31.363580v1.full.pdf) about  OmicPioneer-sc an open-source data visualization/analysis package that integrates dimensionality-reduction plots (DRPs) such as t-SNE and UMAP with Next-Generation Clustered Heat Maps (NGCHMs) and Pathway Visualization Modules (PVMs) in a seamless, highly interactive exploratory environment. They have also stated that they have implemented plug-in status or links with a number of capable bioinformatic environments, including cBioPortal. So is there any example dataset where tSNE, UMAP and PCA plots are visualised? Can you please help us with the example dataset if there is any.

Thanks and regards,

Tulasi S

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Jessica Singh

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[Tulasi S]

Thank you Jessica for your reply. Will look into the example and get back to you if I have any questions.

Regards,

Tulasi S