{ "_id": "6aade6753d719c1f840783ce", "Package": "cascadeR", "Title": "Shiny App to Explore Single-Cell Analysis", "Version": "0.99.0", "Authors@R": "c(\nperson(\"Apratim\", \"Mitra\", , \"apratim.mitra@gmail.com\",\nrole = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0003-3279-0054\")),\nperson(\"Ryan\", \"Dale\", , \"ryan.dale@nih.gov\",\nrole = c(\"fnd\"), comment = c(ORCID = \"0000-0003-2664-3744\"))\n)", "Description": "Interactive and modular shiny app for single-cell and\nspatial transcriptomic data exploration and management.\nVisualize cell clusters or groups using interactive cell\nembeddings, e.g. UMAP or t-SNE, or spatial views. Explore cell\ncomposition and quality control metrics using the metadata\nviewer module. Investigate the effect of clustering resolutions\nor compare annotation sources using cluster tree. Visualize\ngene expression using cell embeddings or in spatial context\nwith feature plots and coexpression plots or in cell clusters\nusing dotplots, violin plots. Manage marker tables from\nsingle-cell or pseudo-bulk analyses and track genes of interest\nusing the gene scratchpad. Choose interesting cells with lasso\nselection directly from interactive plots and export for\ndownstream analysis. Slice and dice datasets with custom\nfilters based on cell metadata, gene expression or lasso\nselections. Efficiently handle large datasets using custom\ndownsampling controls. CascadeR has cross-ecosystem\ncompatibility with support for Seurat, SingleCellExperiment and\nAnnData objects. In addition, the app includes an integrated\nplatform to manage multiple projects and user access that can\nbe run on a central server to share with collaborators.", "License": "MIT + file LICENSE", "Encoding": "UTF-8", "Roxygen": "list(markdown = TRUE)", "VignetteBuilder": "knitr", "BugReports": "https://github.com/NICHD-BSPC/cascadeR/issues", "biocViews": "Software, SingleCell, Spatial, Transcriptomics,\nGeneExpression, Visualization, DifferentialExpression,\nShinyApps, GUI", "URL": "https://nichd-bspc.github.io/cascadeR/", "Config/roxygen2/version": "8.1.0", "Config/pak/sysreqs": "cmake libfontconfig1-dev libfreetype6-dev\nlibglpk-dev make libicu-dev libpng-dev libuv1-dev libxml2-dev\nlibssl-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", 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