Package: carnation
Title: Interactive Exploration & Management of RNA-Seq Analyses
Version: 1.0.0
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 (>= 4.5.0)
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
Config/pak/sysreqs: libcairo2-dev cmake libfontconfig1-dev
        libfreetype6-dev libglpk-dev make libmagick++-dev gsfonts
        libbz2-dev libicu-dev liblzma-dev libpng-dev libuv1-dev
        libxml2-dev libssl-dev perl python3 xz-utils zlib1g-dev
Repository: https://bioc-release.r-universe.dev
Date/Publication: 2026-04-28 13:06:21 UTC
RemoteUrl: https://github.com/bioc/carnation
RemoteRef: RELEASE_3_23
RemoteSha: 2ff883eb4ec105813d70887735930914088a54d3
NeedsCompilation: no
Packaged: 2026-04-29 18:42:32 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; ; 2026-04-29 18:57:52 UTC; windows
