Package: carnation
Title: Interactive Exploration & Management of RNA-Seq Analyses
Version: 0.99.9
Authors@R: 
    c(
        person("Apratim", "Mitra", , "apratim.mitra@nih.gov",
               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: This package provides a 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: 2026-03-18 03:22:08 UTC
RemoteUrl: https://github.com/bioc/carnation
RemoteRef: HEAD
RemoteSha: fa3b19951576877f84354ce091944448ba7624ad
NeedsCompilation: no
Packaged: 2026-03-18 06:12:16 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@nih.gov>
Built: R 4.6.0; ; 2026-03-18 06:16:51 UTC; windows
