PlaqView
Authors: Wei Feng Ma
Abstract: This app is designed for the storage and exploration of advanced single-cell sequencing data. First load the dataset on the 'select dataset' tab, then launch plaqview using the green popup icon. Each panel is designed to explore a different aspect of the dataset. In 'quick gene lookup', users can input a gene of interest and it will render the plot in the desired configuration. 'labeling method' is for annotation method selection, a common problem in single-cell sequencing datasets. 'trajectory method' is for differentiation mapping, and so on!
Full Description: PlaqView is a standalone, interactive, and reproducible Shiny- and R-based tool to explore single-cell RNA-sequencing data of human coronary artery samples. Our goal is to make these valuable data analytic tools publicly available to non-bioinformaticians. This is an open-sourced tool that is freely available and can be modified for other scRNA-seq data.
Reproducibility and Code Availability
PlaqView is designed to be open-source and publicly available and serve as a template for other scRNA-seq analysis pipelines. The code scripts are available on our GitHub Page. This application calls for .rds datafiles that are too large to host on Github, but you can find them at the source codes on GitHub or by emailing us, we will get back to you in 24hrs. To Run this application successfully, place all the .rds object file in the folder/subdiretory called 'data.'
Packages Used
Seurat, Monocle3, Tidyverse, EnrichR, scCATCH, Shiny. See session info for detailed version and package history.
About Our Lab
The Miller Lab is a part of the Center for Public Health Genomics of the University of Virginia, School of Medicine in Charlottesville, VA. Our lab focuses on finding novel risk factors and mechanisms of heart diseases using next-generation sequencing techniques. For questions about our lab, please contact us here. For questions about PlaqView, raise a ticket in our GitHub Page.
About RStudio Cloud Project:
UVA has dedicated Rstudio Server (especially for patient data). I am unsure if I can host my project on the Rstudio Cloud Project without prior authorization.
Keywords: single-cell, big-data, genomics, cardiovascular, genetics, drug, discovery
Shiny app: https://millerlab.shinyapps.io/PlaqView/
Repo: GitHub - MillerLab-CPHG/PlaqView: This is a standalone interactive Shiny tool to analyze and explore single-cell RNA-seq data from human coronary artery.
RStudio Cloud:
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