{
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  "Package": "Capsule",
  "Type": "Package",
  "Title": "Comprehensive Reproducibility Framework for R and Bioinformatics\nAnalysis",
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  "Authors@R": "person(given = \"Abu\",\nfamily = \"SAADAT\",\nrole = c(\"aut\", \"cre\"),\nemail = \"saadatabu1996@gmail.com\",\ncomment = c(ORCID = \"https://orcid.org/0000-0001-9636-2513\",\naffiliation = \"Università degli Studi della Campania Luigi Vanvitelli\"))",
  "Description": "A comprehensive reproducibility framework designed for R\nand bioinformatics workflows. Automatically captures the entire\nanalysis environment including R session info, package\nversions, external tool versions (Samtools, STAR, BWA, etc.),\nconda environments, reference genomes, data provenance with\nsmart checksumming for large files, parameter choices, random\nseeds, and hardware specifications. Generates executable\nscripts with Docker, Singularity, and renv configurations.\nIntegrates with workflow managers (Nextflow, Snakemake, WDL,\nCWL) to ensure complete reproducibility of computational\nresearch workflows.",
  "License": "MIT + file LICENSE",
  "Encoding": "UTF-8",
  "BugReports": "https://github.com/SAADAT-Abu/Capsule/issues",
  "RoxygenNote": "7.3.3",
  "Repository": "https://saadat-abu.r-universe.dev",
  "Date/Publication": "2025-12-28 21:24:43 UTC",
  "RemoteUrl": "https://github.com/SAADAT-Abu/Capsule",
  "RemoteRef": "HEAD",
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    "User": "root"
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    "create_repro_report",
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    "get_data_lineage",
    "get_param_history",
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    "get_seed_history",
    "get_tool_versions",
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    "restore_seed",
    "set_seed",
    "snapshot_packages",
    "snapshot_workflow",
    "track_conda_env",
    "track_data",
    "track_external_tools",
    "track_params",
    "track_reference_genome",
    "verify_data"
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      "title": "Capture Environment State",
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      ]
    },
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      ]
    },
    {
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      "title": "Capture Complete Session Information",
      "topics": [
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      ]
    },
    {
      "page": "capture_system_libraries",
      "title": "Capture System Libraries",
      "topics": [
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      ]
    },
    {
      "page": "compare_snapshots",
      "title": "Compare Two Workflow Snapshots",
      "topics": [
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      ]
    },
    {
      "page": "create_renv_lockfile",
      "title": "Create renv Lockfile",
      "topics": [
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      ]
    },
    {
      "page": "create_repro_report",
      "title": "Create Reproducibility Report",
      "topics": [
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      ]
    },
    {
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      "title": "Generate CWL (Common Workflow Language) Input",
      "topics": [
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      ]
    },
    {
      "page": "export_for_nextflow",
      "title": "Export Capsule Data for Nextflow",
      "topics": [
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      ]
    },
    {
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      "title": "Export Capsule Data for Snakemake",
      "topics": [
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      ]
    },
    {
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      "topics": [
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      ]
    },
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      "topics": [
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    },
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      "topics": [
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    },
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