Package: carnation
Title: Shiny App to Explore RNA-Seq Analysis
Version: 0.99.8
Authors@R: 
    c(
        person("Apratim", "Mitra", , "apratim.mitra@nih.gov",
               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 Shiny dashboard app that can be used to
        explore RNA-Seq analysis results including differential
        expression (DE), functional enrichment and pattern analysis.
        Several visualizations are implemented to provide a
        wide-ranging view of data sets. For DE analysis, we provide PCA
        plot, MA plot, Upset plot & heatmaps, in addition to a highly
        customizable gene plot.  Seven different visualizations are
        available for functional enrichment analysis, and we also
        support gene pattern analysis. In addition, the app provides a
        platform to manage multiple projects and user groups that can
        be run on a central server.
License: MIT + file LICENSE
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.3
Depends: R (>= 4.4.0)
Imports: BiocParallel, colorspace, ComplexUpset, dendextend, DESeq2,
        dplyr, DT, enrichplot, GeneTonic, ggplot2, ggrepel, heatmaply,
        htmltools, igraph, methods, MatrixGenerics, plotly, reticulate,
        RColorBrewer, rintrojs, scales, shiny, shinyBS,
        shinycssloaders, shinymanager, shinythemes, shinyWidgets,
        sortable, SummarizedExperiment, tools, utils, viridisLite,
        visNetwork, yaml
Suggests: airway, BiocStyle, DEGreport, GenomicFeatures, goseq, knitr,
        org.Hs.eg.db, rmarkdown, testthat
VignetteBuilder: knitr
URL: https://nichd-bspc.github.io/carnation/
BugReports: https://github.com/NICHD-BSPC/carnation/issues
biocViews: GUI, GeneExpression, Software, ShinyApps, GO, Transcription,
        Transcriptomics, Visualization, DifferentialExpression,
        Pathways, GeneSetEnrichment
Repository: https://bioc.r-universe.dev
Date/Publication: 2026-01-30 15:48:44 UTC
RemoteUrl: https://github.com/bioc/carnation
RemoteRef: HEAD
RemoteSha: e7954aebc6c9390fdd09300b63519fa9a40dfad3
NeedsCompilation: no
Packaged: 2026-02-14 02:51:30 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@nih.gov>
Built: R 4.6.0; ; 2026-02-14 03:00:49 UTC; windows
