Package: carnation
Title: Interactive Exploration & Management of RNA-Seq Analyses
Version: 1.1.0
Authors@R: 
    c(
        person("Apratim", "Mitra", , "apratim.mitra@gmail.com",
               role = c("aut", "cre"), comment = c(ORCID = "0000-0003-3279-0054")),
        person(c("Matthew", "Tyler"), "Menold", , "matthew.menold@gmail.com",
               role = c("ctb"), comment = c(ORCID = "0009-0007-4728-2470")),
        person("Ryan", "Dale", , "ryan.dale@nih.gov",
               role = c("fnd"), comment = c(ORCID = "0000-0003-2664-3744"))
    )
Description: Highly interactive & modular shiny app to
    explore three facets of RNA-Seq analysis: 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. Genes of interest can
    be tracked across all modules using the gene scratchpad. In addition,
    carnation provides 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)
RoxygenNote: 7.3.3
Depends: R (>= 4.6.0)
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
git_url: https://git.bioconductor.org/packages/carnation
git_branch: devel
git_last_commit: 4789c1f
git_last_commit_date: 2026-04-28
Repository: Bioconductor 3.24
Date/Publication: 2026-05-18
NeedsCompilation: no
Packaged: 2026-05-18 21:29:53 UTC; biocbuild
Author: Apratim Mitra [aut, cre] (ORCID:
    <https://orcid.org/0000-0003-3279-0054>),
  Matthew Tyler Menold [ctb] (ORCID:
    <https://orcid.org/0009-0007-4728-2470>),
  Ryan Dale [fnd] (ORCID: <https://orcid.org/0000-0003-2664-3744>)
Maintainer: Apratim Mitra <apratim.mitra@gmail.com>
Built: R 4.6.0; ; 2026-05-19 04:44:38 UTC; unix
