AlzApp: A Tool for Exploration and Visualization of Frontotemporal Dementia scRNAseq Data

Live app at: https://inciteprojects.idea.rpi.edu/alzapp/app/alzapp/

This R Shiny application is a data-browsing tool that exposes a large corpus of scRNAseq data from organoid models of frontotemporal dementia and isogenic controls to the biologist and the general user.

The Dataset

The scRNAseq data set we draw on in the app was originally generated in an experimental suite presented in Bowles et al. (2021). This transcriptomic data represents gene expression levels and cell attributes for a large body of 370,000 individual cells, encompassing a set of mutant cells with a mutation in the MAPT gene (Tau V337M) that is implicated in frontotemporal dementia (FTD), as well as the equivalent CRISPR-corrected control cells.

Usage

See the usage guide in man/ for instructions on how to prepare and upload your own single-cell dataset for usage with this application (under development; coming soon).

The app enables the user to analyze subsets of a complete single-cell dataset based on various combinations of cell attributes (e.g. Cell type, mutant vs. control), or by querying an individual gene of interest. The alternate top-level views provide a range of data browsing modes for the researcher to aid in characterization of genetic perturbations associated with the disease or condition their dataset was generated to characterize.

Visit our GitHub Wiki for more details and background on the app.