Package: carnation
Title: Interactive Exploration & Management of RNA-Seq Analyses
Version: 0.99.11
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 (>= 4.4.0)
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: 2026-04-20 19:52:24 UTC
RemoteUrl: https://github.com/bioc/carnation
RemoteRef: HEAD
RemoteSha: 6945a1e6fb392481139045991db2cd7a4fcf8bdf
NeedsCompilation: no
Packaged: 2026-04-21 07:10:22 UTC; root
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; ; 2026-04-21 07:16:18 UTC; windows
