PlaqView 2.0: A comprehensive web portal for cardiovascular single-cell genomics

Single-cell RNA-seq (scRNA-seq) is a powerful genomics technology to interrogate the cellular composition and behaviors of complex systems. While the number of scRNA-seq datasets and available computational analysis tools have grown exponentially, there are limited systematic data sharing strategies...

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Bibliographic Details
Published in:Frontiers in cardiovascular medicine 2022-08, Vol.9, p.969421
Main Authors: Ma, Wei Feng, Turner, Adam W, Gancayco, Christina, Wong, Doris, Song, Yipei, Mosquera, Jose Verdezoto, Auguste, Gaëlle, Hodonsky, Chani J, Prabhakar, Ajay, Ekiz, H Atakan, van der Laan, Sander W, Miller, Clint L
Format: Article
Language:English
Subjects:
cardiovascular
Cardiovascular Medicine
genomics
scRNA-seq
single-cell
web portal
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Summary:Single-cell RNA-seq (scRNA-seq) is a powerful genomics technology to interrogate the cellular composition and behaviors of complex systems. While the number of scRNA-seq datasets and available computational analysis tools have grown exponentially, there are limited systematic data sharing strategies to allow rapid exploration and re-analysis of single-cell datasets, particularly in the cardiovascular field. We previously introduced PlaqView, an open-source web portal for the exploration and analysis of published atherosclerosis single-cell datasets. Now, we introduce PlaqView 2.0 (www.plaqview.com), which provides expanded features and functionalities as well as additional cardiovascular single-cell datasets. We showcase improved PlaqView functionality, backend data processing, user-interface, and capacity. PlaqView brings new or improved tools to explore scRNA-seq data, including gene query, metadata browser, cell identity prediction, RNA-trajectory analysis, and drug-gene interaction prediction. PlaqView serves as one of the largest central repositories for cardiovascular single-cell datasets, which now includes data from human aortic aneurysm, gene-specific mouse knockouts, and healthy references. PlaqView 2.0 brings advanced tools and high-performance computing directly to users without the need for any programming knowledge. Lastly, we outline steps to generalize and repurpose PlaqView's framework for single-cell datasets from other fields.
ISSN:2297-055X
2297-055X
DOI:10.3389/fcvm.2022.969421