{
  "_id": "6a17ef59acfb0bcc41da6005",
  "Package": "DeeDeeExperiment",
  "Title": "DeeDeeExperiment: An S4 Class for managing and exploring omics\nanalysis results",
  "Version": "1.3.0",
  "Authors@R": "c(\nperson(\ngiven = \"Najla\", family = \"Abassi\", role = c(\"aut\", \"cre\"),\nemail = \"abassi.nejla96@gmail.com\",\ncomment = c(ORCID = \"0000-0001-8357-0938\")\n),\nperson(\ngiven = \"Lea\", family = \"Schwarz\", role = c(\"aut\"),\nemail = \"lea.schwarz@uni-mainz.de\",\ncomment = c(ORCID = \"0000-0003-2554-0583\")\n),\nperson(\ngiven = \"Federico\", family = \"Marini\", role = c(\"aut\"),\nemail = \"marinif@uni-mainz.de\",\ncomment = c(ORCID = \"0000-0003-3252-7758\")\n)\n)",
  "Description": "DeeDeeExperiment is an S4 class extending the\nSingleCellExperiment class, designed to integrate and manage\nomics analysis results. It introduces two dedicated slots to\nstore Differential Expression Analysis (DEA) results and\nFunctional Enrichment Analysis (FEA) results, providing a\nstructured approach for downstream analysis.",
  "License": "MIT + file LICENSE",
  "Encoding": "UTF-8",
  "Roxygen": "list(markdown = TRUE)",
  "RoxygenNote": "7.3.3",
  "VignetteBuilder": "knitr",
  "URL": "https://github.com/imbeimainz/DeeDeeExperiment",
  "BugReports": "https://github.com/imbeimainz/DeeDeeExperiment/issues",
  "biocViews": "Software, Infrastructure, DataRepresentation,\nGeneExpression, Transcription, Transcriptomics,\nDifferentialExpression, Pathways, GO",
  "Config/testthat/edition": "3",
  "Config/pak/sysreqs": "zlib1g-dev",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 13:05:18 UTC",
  "RemoteUrl": "https://github.com/bioc/DeeDeeExperiment",
  "RemoteRef": "HEAD",
  "RemoteSha": "9bf542794ec216afcea72e63eb7a24b44a931e9a",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-05-28 06:36:25 UTC",
    "User": "root"
  },
  "Author": "Najla Abassi [aut, cre] (ORCID:\n<https://orcid.org/0000-0001-8357-0938>),\nLea Schwarz [aut] (ORCID: <https://orcid.org/0000-0003-2554-0583>),\nFederico Marini [aut] (ORCID: <https://orcid.org/0000-0003-3252-7758>)",
  "Maintainer": "Najla Abassi <abassi.nejla96@gmail.com>",
  "MD5sum": "0f4668599d64737d6000f86ae6df39ff",
  "_user": "bioc",
  "_type": "src",
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  "_created": "2026-05-28T06:36:25.000Z",
  "_published": "2026-05-28T07:31:37.136Z",
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    "linkedin": "in/najla-abassi",
    "description": "Bioinformatician/Research Associate",
    "uuid": 112277365,
    "orcid": "0000-0001-8357-0938"
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    "infrastructure",
    "datarepresentation",
    "geneexpression",
    "transcription",
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    "differentialexpression",
    "pathways",
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    "description": "Software for the analysis and comprehension of high-throughput genomic data"
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    "source": "https://www.bioconductor.org/packages/stats/bioc/DeeDeeExperiment"
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  "_devurl": "https://github.com/imbeimainz/deedeeexperiment",
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  "_assets": [
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    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
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    "extra/NEWS.html",
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    "extra/readme.md",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/imbeimainz/deedeeexperiment",
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "addDEA",
    "addFEA",
    "addScenarioInfo",
    "DeeDeeExperiment",
    "export_result_for_dde",
    "getDEA",
    "getDEAInfo",
    "getDEAInfo<-",
    "getDEAList",
    "getDEANames",
    "getFEA",
    "getFEAInfo",
    "getFEAInfo<-",
    "getFEAList",
    "getFEANames",
    "limma_list_for_dde",
    "linkDEAandFEA",
    "muscat_list_for_dde",
    "removeDEA",
    "removeFEA",
    "renameDEA",
    "renameFEA",
    "show",
    "supported_fea_formats"
  ],
  "_datasets": [
    {
      "name": "clusterPro_res",
      "title": "'clusterPro_res'",
      "object": "clusterPro_res",
      "file": "clusterPro_res.RData",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "de_limma",
      "title": "A sample 'MArrayLM' object",
      "object": "de_limma",
      "file": "de_limma.RData",
      "class": [
        "MArrayLM"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "de_named_list",
      "title": "de_named_list",
      "object": "de_named_list",
      "file": "de_named_list.RData",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "dge_exact_IFNg_both",
      "title": "A sample 'DGEExact' object",
      "object": "DGEExact_IFNg_both",
      "file": "DGEExact_IFNg_both.RData",
      "class": [
        "DGEExact"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "dge_exact_IFNg_naive",
      "title": "A sample 'DGEExact' object",
      "object": "DGEExact_IFNg_naive",
      "file": "DGEExact_IFNg_naive.RData",
      "class": [
        "DGEExact"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "dge_exact_Salm_both",
      "title": "A sample 'DGEExact' object",
      "object": "DGEExact_Salm_both",
      "file": "DGEExact_Salm_both.RData",
      "class": [
        "DGEExact"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "dge_exact_Salm_naive",
      "title": "A sample 'DGEExact' object",
      "object": "DGEExact_Salm_naive",
      "file": "DGEExact_Salm_naive.RData",
      "class": [
        "DGEExact"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "dge_lrt_IFNg_both",
      "title": "A sample 'DGELRT' object",
      "object": "dgeLRT_IFNg_both",
      "file": "dgeLRT_IFNg_both.RData",
      "class": [
        "DGELRT"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "dge_lrt_IFNg_naive",
      "title": "A sample 'DGELRT' object",
      "object": "dgeLRT_IFNg_naive",
      "file": "dgeLRT_IFNg_naive.RData",
      "class": [
        "DGELRT"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "dge_lrt_Salm_both",
      "title": "A sample 'DGELRT' object",
      "object": "dgeLRT_Salm_both",
      "file": "dgeLRT_Salm_both.RData",
      "class": [
        "DGELRT"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "dge_lrt_Salm_naive",
      "title": "A sample 'DGELRT' object",
      "object": "dgeLRT_Salm_naive",
      "file": "dgeLRT_Salm_naive.RData",
      "class": [
        "DGELRT"
      ],
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      "table": false,
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      "title": "'enrichr_res'",
      "object": "enrichr_res",
      "file": "enrichr_res.RData",
      "class": [
        "list"
      ],
      "fields": [],
      "table": true,
      "tojson": true
    },
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      "name": "fgseaRes",
      "title": "'fgseaRes'",
      "object": "fgseaRes",
      "file": "fgseaRes.RData",
      "class": [
        "data.table",
        "data.frame"
      ],
      "fields": [
        "pathway",
        "pval",
        "padj",
        "ES",
        "NES",
        "nMoreExtreme",
        "size",
        "leadingEdge"
      ],
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      "table": true,
      "tojson": true
    },
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      "title": "'gost_res'",
      "object": "gost_res",
      "file": "gost_res.RData",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
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      "name": "gsea_res",
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      "object": "gsea_res",
      "file": "gsea_res.RData",
      "class": [
        "gseaResult"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "IFNg_both",
      "title": "A sample 'DESeqResults' object",
      "object": "dea_IFNg_both",
      "file": "dea_IFNg_both.RData",
      "class": [
        "DESeqResults"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "IFNg_naive",
      "title": "A sample 'DESeqResults' object",
      "object": "dea_IFNg_naive",
      "file": "dea_IFNg_naive.RData",
      "class": [
        "DESeqResults"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "muscat_res",
      "title": "'muscat_res'",
      "object": "muscat_pbDS_res",
      "file": "muscat_pbDS_res.RData",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "Salm_both",
      "title": "A sample 'DESeqResults' object",
      "object": "dea_Salm_both",
      "file": "dea_Salm_both.RData",
      "class": [
        "DESeqResults"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "Salm_naive",
      "title": "A sample 'DESeqResults' object",
      "object": "dea_Salm_naive",
      "file": "dea_Salm_naive.RData",
      "class": [
        "DESeqResults"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "topGO_results_list",
      "title": "'topGO_results_list'",
      "object": "topGO_results_list",
      "file": "topGO_results_list.RData",
      "class": [
        "list"
      ],
      "fields": [],
      "table": true,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "clusterPro_res",
      "title": "'clusterPro_res'",
      "concept": [
        "enrich_resus"
      ],
      "topics": [
        "clusterPro_res"
      ]
    },
    {
      "page": "dd_list_original",
      "title": "dd_list_original",
      "topics": [
        "dd_list_original"
      ]
    },
    {
      "page": "de_limma",
      "title": "A sample 'MArrayLM' object",
      "topics": [
        "de_limma"
      ]
    },
    {
      "page": "de_named_list",
      "title": "de_named_list",
      "topics": [
        "de_named_list"
      ]
    },
    {
      "page": "DeeDeeExperiment",
      "title": "The DeeDeeExperiment class",
      "topics": [
        ".DeeDeeExperiment",
        "DeeDeeExperiment",
        "DeeDeeExperiment-class"
      ]
    },
    {
      "page": "DeeDeeExperiment-methods",
      "title": "Methods for DeeDeeExperiment objects",
      "topics": [
        "addDEA",
        "addDEA,DeeDeeExperiment-method",
        "addFEA",
        "addFEA,DeeDeeExperiment-method",
        "addScenarioInfo",
        "addScenarioInfo,DeeDeeExperiment-method",
        "DeeDeeExperiment-methods",
        "getDEA",
        "getDEA,DeeDeeExperiment-method",
        "getDEAInfo",
        "getDEAInfo,DeeDeeExperiment-method",
        "getDEAInfo<-",
        "getDEAInfo<-,DeeDeeExperiment-method",
        "getDEAList",
        "getDEAList,DeeDeeExperiment-method",
        "getDEANames",
        "getDEANames,DeeDeeExperiment-method",
        "getFEA",
        "getFEA,DeeDeeExperiment-method",
        "getFEAInfo",
        "getFEAInfo,DeeDeeExperiment-method",
        "getFEAInfo<-",
        "getFEAInfo<-,DeeDeeExperiment-method",
        "getFEAList",
        "getFEAList,DeeDeeExperiment-method",
        "getFEANames",
        "getFEANames,DeeDeeExperiment-method",
        "linkDEAandFEA",
        "linkDEAandFEA,DeeDeeExperiment-method",
        "removeDEA",
        "removeDEA,DeeDeeExperiment-method",
        "removeFEA",
        "removeFEA,DeeDeeExperiment-method",
        "renameDEA",
        "renameDEA,DeeDeeExperiment-method",
        "renameFEA",
        "renameFEA,DeeDeeExperiment-method"
      ]
    },
    {
      "page": "DeeDeeExperiment-misc",
      "title": "Miscellaneous DeeDeeExperiment methods",
      "topics": [
        "DeeDeeExperiment-misc",
        "show,DeeDeeExperiment-method",
        "summary,DeeDeeExperiment-method"
      ]
    },
    {
      "page": "DeeDeeExperiment-pkg",
      "title": "DeeDeeExperiment",
      "topics": [
        "DeeDeeExperiment-package",
        "DeeDeeExperiment-pkg"
      ]
    },
    {
      "page": "dge_exact_IFNg_both",
      "title": "A sample 'DGEExact' object",
      "concept": [
        "edgeRresus"
      ],
      "topics": [
        "dge_exact_IFNg_both"
      ]
    },
    {
      "page": "dge_exact_IFNg_naive",
      "title": "A sample 'DGEExact' object",
      "concept": [
        "edgeRresus"
      ],
      "topics": [
        "dge_exact_IFNg_naive"
      ]
    },
    {
      "page": "dge_exact_Salm_both",
      "title": "A sample 'DGEExact' object",
      "concept": [
        "edgeRresus"
      ],
      "topics": [
        "dge_exact_Salm_both"
      ]
    },
    {
      "page": "dge_exact_Salm_naive",
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