Package: cascadeR 0.99.0

cascadeR: Shiny App to Explore Single-Cell Analysis

Interactive and modular shiny app for single-cell and spatial transcriptomic data exploration and management. Visualize cell clusters or groups using interactive cell embeddings, e.g. UMAP or t-SNE, or spatial views. Explore cell composition and quality control metrics using the metadata viewer module. Investigate the effect of clustering resolutions or compare annotation sources using cluster tree. Visualize gene expression using cell embeddings or in spatial context with feature plots and coexpression plots or in cell clusters using dotplots, violin plots. Manage marker tables from single-cell or pseudo-bulk analyses and track genes of interest using the gene scratchpad. Choose interesting cells with lasso selection directly from interactive plots and export for downstream analysis. Slice and dice datasets with custom filters based on cell metadata, gene expression or lasso selections. Efficiently handle large datasets using custom downsampling controls. CascadeR has cross-ecosystem compatibility with support for Seurat, SingleCellExperiment and AnnData objects. In addition, the app includes an integrated platform to manage multiple projects and user access that can be run on a central server to share with collaborators.

Authors:Apratim Mitra [aut, cre], Ryan Dale [fnd]