Package: cascadeR
Title: Shiny App to Explore Single-Cell Analysis
Version: 0.99.0
Authors@R: 
    c(
        person("Apratim", "Mitra", , "apratim.mitra@gmail.com",
               role = c("aut", "cre"), comment = c(ORCID = "0000-0003-3279-0054")),
        person("Ryan", "Dale", , "ryan.dale@nih.gov",
               role = c("fnd"), comment = c(ORCID = "0000-0003-2664-3744"))
    )
Description: 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.
License: MIT + file LICENSE
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
Imports: anndata, ape, clustree, colorspace, data.table, dplyr, DT,
        ggplot2, ggraph, graphics, grid, htmltools, Matrix, methods,
        plotly, RColorBrewer, readr, reshape2, reticulate, rintrojs,
        rlang, scales, Seurat, SeuratObject, SingleCellExperiment,
        SummarizedExperiment, shiny, shinyBS, shinycssloaders, shinyjs,
        shinythemes, shinyWidgets, sortable, stats, tidyr, UpSetR,
        utils, viridis, yaml
Suggests: BiocStyle, knitr, rmarkdown, shinymanager, testthat
VignetteBuilder: knitr
BugReports: https://github.com/NICHD-BSPC/cascadeR/issues
biocViews: Software, SingleCell, Spatial, Transcriptomics,
        GeneExpression, Visualization, DifferentialExpression,
        ShinyApps, GUI
URL: https://nichd-bspc.github.io/cascadeR/
Config/roxygen2/version: 8.1.0
Config/pak/sysreqs: cmake libfontconfig1-dev libfreetype6-dev
        libglpk-dev make libicu-dev libpng-dev libuv1-dev libxml2-dev
        libssl-dev python3 libx11-dev zlib1g-dev
Repository: https://biocstaging.r-universe.dev
Date/Publication: 2026-09-18 22:52:46 UTC
RemoteUrl: https://github.com/BiocStaging/cascadeR
RemoteRef: HEAD
RemoteSha: 3c944e1f7344b998eb09c0419f7bc952ec862347
NeedsCompilation: no
Packaged: 2026-09-19 01:24:54 UTC; root
Author: Apratim Mitra [aut, cre] (ORCID:
    <https://orcid.org/0000-0003-3279-0054>),
  Ryan Dale [fnd] (ORCID: <https://orcid.org/0000-0003-2664-3744>)
Maintainer: Apratim Mitra <apratim.mitra@gmail.com>