{ "_id": "6a1e9a3a1d7bb097a0a6e27c", "Package": "carnation", "Title": "Interactive Exploration & Management of RNA-Seq Analyses", "Version": "1.1.0", "Authors@R": "c(\nperson(\"Apratim\", \"Mitra\", , \"apratim.mitra@gmail.com\",\nrole = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0003-3279-0054\")),\nperson(c(\"Matthew\", \"Tyler\"), \"Menold\", , \"matthew.menold@gmail.com\",\nrole = c(\"ctb\"), comment = c(ORCID = \"0009-0007-4728-2470\")),\nperson(\"Ryan\", \"Dale\", , \"ryan.dale@nih.gov\",\nrole = c(\"fnd\"), comment = c(ORCID = \"0000-0003-2664-3744\"))\n)", "Description": "Highly interactive & modular shiny app to explore three\nfacets of RNA-Seq analysis: differential expression (DE),\nfunctional enrichment and pattern analysis. Several\nvisualizations are implemented to provide a wide-ranging view\nof data sets. For DE analysis, we provide PCA plot, MA plot,\nUpset plot & heatmaps, in addition to a highly customizable\ngene plot. Seven different visualizations are available for\nfunctional enrichment analysis, and we also support gene\npattern analysis. Genes of interest can be tracked across all\nmodules using the gene scratchpad. In addition, carnation\nprovides an integrated platform to manage multiple projects and\nuser access that can be run on a central server to share with\ncollaborators.", "License": "MIT + file LICENSE", "Encoding": "UTF-8", "Roxygen": "list(markdown = TRUE)", "RoxygenNote": "7.3.3", "VignetteBuilder": "knitr", "URL": "https://nichd-bspc.github.io/carnation/", "BugReports": "https://github.com/NICHD-BSPC/carnation/issues", "biocViews": "GUI, GeneExpression, Software, ShinyApps, GO, Transcription,\nTranscriptomics, Visualization, DifferentialExpression,\nPathways, GeneSetEnrichment", "Config/pak/sysreqs": "libcairo2-dev cmake libfontconfig1-dev\nlibfreetype6-dev libglpk-dev make libmagick++-dev gsfonts\nlibbz2-dev libicu-dev liblzma-dev libpng-dev libuv1-dev\nlibxml2-dev libssl-dev perl python3 xz-utils zlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 18:04:36 UTC", "RemoteUrl": "https://github.com/bioc/carnation", "RemoteRef": "HEAD", "RemoteSha": "4789c1f5fd2ca0228212e8dceeacd2166fcaee06", "NeedsCompilation": "no", "Packaged": { "Date": "2026-06-02 08:41:04 UTC", "User": "root" }, "Author": "Apratim Mitra [aut, cre] (ORCID:\n),\nMatthew Tyler Menold [ctb] (ORCID:\n),\nRyan Dale [fnd] (ORCID: )", "Maintainer": "Apratim Mitra ", "MD5sum": "0e55dfb9a7d32ca0906dceadcb41d73e", "_user": "bioc", "_type": "src", "_file": "carnation_1.1.0.tar.gz", "_fileid": "0a4585f2d7493a9d9fc8c3ab748ea21120b3e50044e64009fb58d949b0cac00b", "_filesize": 5276626, "_sha256": "0a4585f2d7493a9d9fc8c3ab748ea21120b3e50044e64009fb58d949b0cac00b", "_created": "2026-06-02T08:41:04.000Z", "_published": "2026-06-02T08:54:18.902Z", "_jobs": [ { "job": 79032629292, "time": 356, "config": "bioc-checks", "r": "4.6.0", "check": "NOTE", "artifact": "7353104666" }, { "job": 79032629409, "time": 598, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "WARNING", "artifact": "7353192798" }, { "job": 79032629309, "time": 691, "config": "linux-release-x86_64", "r": 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"https://github.com/r-universe/bioc/actions/runs/26808213076", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/bioc/carnation", "_commit": { "id": "4789c1f5fd2ca0228212e8dceeacd2166fcaee06", "author": "Apratim Mitra ", "committer": "Apratim Mitra ", "message": "Merge remote-tracking branch 'upstream/devel' into devel\n", "time": 1777399476 }, "_maintainer": { "name": "Apratim Mitra", "email": "apratim.mitra@gmail.com", "login": "mitraak", "description": "", "uuid": 16709900, "orcid": "0000-0003-3279-0054" }, "_distro": "noble", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.5.0", "role": "Depends" }, { "package": "BiocParallel", "role": "Imports" }, { "package": "colorspace", "role": "Imports" }, { "package": "ComplexUpset", "role": "Imports" }, { "package": "dendextend", "role": "Imports" }, { "package": "DESeq2", "role": "Imports" }, { "package": "dplyr", "role": "Imports" }, { "package": "DT", "role": "Imports" }, { 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dexamethasone on smooth muscle cells", "object": "res_dex", "file": "res_dex.RData", "class": [ "DESeqResults" ], "fields": [], "table": false, "tojson": false } ], "_help": [ { "page": "add_metadata", "title": "Add metadata to counts data frame", "topics": [ "add_metadata" ] }, { "page": "add.set.column", "title": "Add set column to UpSet plot matrix", "topics": [ "add.set.column" ] }, { "page": "alluvialmod", "title": "Alluvial plot module", "topics": [ "alluvialmod", "alluvialServer", "alluvialUI" ] }, { "page": "check_user_access", "title": "Get data areas a user has access to", "topics": [ "check_user_access" ] }, { "page": "cnetmod", "title": "Cnetplot module", "topics": [ "cnetmod", "cnetPlotServer", "cnetPlotUI" ] }, { "page": "create_access_yaml", "title": "Create access yaml", "topics": [ "create_access_yaml" ] }, { "page": "degmod", "title": "Pattern plot module", "topics": [ "degmod", "patternPlotServer", "patternPlotUI" ] }, { "page": "degpatterns_dex", "title": "A 'degPatterns' object for differentially expressed genes in the dexamethasone treatment comparison.", "topics": [ "degpatterns_dex" ] }, { "page": "dendromod", "title": "Dendrogram module", "topics": [ "dendrogramServer", "dendrogramUI", "dendromod" ] }, { "page": "distillmod", "title": "Distilled enrichment map module", "topics": [ "distillmod", "distillPlotServer", "distillPlotUI" ] }, { "page": "dlmod", "title": "Download button module", "topics": [ "dlmod", "downloadButtonServer", "downloadButtonUI" ] }, { "page": "dummy_genetonic", "title": "Make dummy GeneTonic object", "topics": [ "dummy_genetonic" ] }, { "page": "emapmod", "title": "Enrichment map plot module", "topics": [ "emapmod", "enrichmapServer", "enrichmapUI" ] }, { "page": "enrich_to_genetonic", "title": "Convert enrichResult to GeneTonic object", "topics": [ "enrich_to_genetonic" ] }, { "page": "eres_cell", "title": "An 'enrichResult' object for differentially expressed genes in the cell line comparison.", "topics": [ "eres_cell" ] }, { "page": "eres_dex", "title": "An 'enrichResult' object for differentially expressed genes in the dexamethasone treatment comparison.", "topics": [ "eres_dex" ] }, { "page": "format_genes", "title": "format gene names to look pretty in table output", "topics": [ "format_genes" ] }, { "page": "fromList.with.names", "title": "Prepare list for UpSet plots, but include rownames", "topics": [ "fromList.with.names" ] }, { "page": "funenrichmod", "title": "Functional enrichment module", "topics": [ "enrichServer", "enrichUI", "funenrichmod" ] }, { "page": "fuzzymod", "title": "Fuzzy enrichment map module", "topics": [ "fuzzymod", "fuzzyPlotServer", "fuzzyPlotUI" ] }, { "page": "geneplotmod", "title": "Gene plot module", "topics": [ "geneplotmod", "genePlotServer", "genePlotUI" ] }, { "page": "get_access_path", "title": "Get path to access yaml file", "topics": [ "get_access_path" ] }, { "page": "get_config", "title": "Get config", "topics": [ "get_config" ] }, { "page": 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] }, { "page": "run_carnation", "title": "Carnation", "topics": [ "run_carnation" ] }, { "page": "save_access_yaml", "title": "Save access yaml to file", "topics": [ "save_access_yaml" ] }, { "page": "savemod", "title": "Save object module UI", "topics": [ "savemod", "saveServer", "saveUI" ] }, { "page": "scattermod", "title": "Scatterplot module", "topics": [ "scattermod", "scatterPlotServer", "scatterPlotUI" ] }, { "page": "set_config", "title": "Set config", "topics": [ "set_config" ] }, { "page": "settingsmod", "title": "Settings module", "topics": [ "settingsmod", "settingsServer", "settingsUI" ] }, { "page": "summarize_res_list", "title": "Combine everything in the results list into a single table", "topics": [ "summarize_res_list" ] }, { "page": "sumovmod", "title": "Summary overview plot module", "topics": [ "sumovmod", "sumovPlotServer", "sumovPlotUI" ] }, { "page": "top.genes", "title": "Get top DE genes by log2FoldChange or adjusted p-value", "topics": [ "top.genes" ] }, { 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