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  "_id": "6a1be7611d7bb097a0a1b23c",
  "Package": "Rega",
  "Title": "R Interface to European Genome-Phenome Archive",
  "Version": "1.1.0",
  "Authors@R": "c(\nperson(\n\"Igor\", \"Cervenka\", , \"igor.cervenka@unibas.ch\", role = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0000-0002-9438-5161\")\n),\nperson(\n\"Athimed\", \"El Taher\", , \"athimed.eltaher@unibas.ch\", role = c(\"aut\"),\ncomment = c(ORCID = \"0000-0003-2424-8476\")\n),\nperson(\n\"Robert\", \"Ivanek\", , \"robert.ivanek@unibas.ch\", role = c(\"aut\"),\ncomment = c(ORCID = \"0000-0002-8403-056X\")\n)\n)",
  "Description": "The European Genome-phenome Archive (EGA) provides\nlong-term storage and controlled sharing of personally\nidentifiable genetic data. The Rega package offers a\nstreamlined and extensible R interface to the EGA API,\nfacilitating the programmatic upload of metadata. GEO-like\nExcel submission template is provided as a default method of\norganizing submission metadata.",
  "License": "Artistic-2.0",
  "URL": "https://github.com/ivanek/Rega",
  "BugReports": "https://github.com/ivanek/Rega/issues",
  "VignetteBuilder": "knitr",
  "biocViews": "Software, Infrastructure, ThirdPartyClient",
  "Config/testthat/edition": "3",
  "Encoding": "UTF-8",
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  "RoxygenNote": "7.3.3",
  "Config/pak/sysreqs": "libicu-dev libsecret-1-dev libssl-dev libnode-dev",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-29 12:57:30 UTC",
  "RemoteUrl": "https://github.com/bioc/Rega",
  "RemoteRef": "HEAD",
  "RemoteSha": "6ca901a186bcaa6e37c8fa82081910ba502c49a6",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-05-31 06:42:47 UTC",
    "User": "root"
  },
  "Author": "Igor Cervenka [aut, cre] (ORCID:\n<https://orcid.org/0000-0002-9438-5161>),\nAthimed El Taher [aut] (ORCID: <https://orcid.org/0000-0003-2424-8476>),\nRobert Ivanek [aut] (ORCID: <https://orcid.org/0000-0002-8403-056X>)",
  "Maintainer": "Igor Cervenka <igor.cervenka@unibas.ch>",
  "MD5sum": "97684b819baad691074b140b1e2e3a09",
  "_user": "bioc",
  "_type": "src",
  "_file": "Rega_1.1.0.tar.gz",
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  "_created": "2026-05-31T06:42:47.000Z",
  "_published": "2026-05-31T07:46:41.166Z",
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  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/26705588551",
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  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/bioc/Rega",
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    "name": "Igor Cervenka",
    "email": "igor.cervenka@unibas.ch",
    "orcid": "0000-0002-9438-5161"
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  "_dependencies": [
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      "package": "askpass",
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      "package": "httr2",
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    },
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  "_updates": [
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  "_bioc": [
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    "thirdpartyclient"
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  "_contributors": [
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      "count": 54,
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  "_userbio": {
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    "type": "organization",
    "name": "Bioconductor",
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
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    "source": "https://www.bioconductor.org/packages/stats/bioc/Rega"
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  "_devurl": "https://github.com/ivanek/rega",
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  "_rbuild": "4.6.0",
  "_assets": [
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    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/readme.html",
    "extra/readme.md",
    "extra/Rega.html",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/ivanek/rega",
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "add_required_str",
    "aliases_formatter",
    "api_function_factory",
    "api_name_to_label",
    "column_table_formatter",
    "create_client",
    "default_parser",
    "default_validator",
    "delete_submission",
    "delete_submission_contents",
    "DELIM_CONVERTERS",
    "ega_oauth",
    "ega_token",
    "extract_api",
    "extract_operation_definitions",
    "extract_resource_name",
    "fetch_files",
    "file_formatter",
    "filter_id_fields",
    "finalise_submission",
    "first_row_to_colnames",
    "fold_column",
    "format_chromosomes",
    "get_chr_group",
    "get_entry_by_title",
    "get_enum",
    "get_formatter",
    "get_formatter_params",
    "get_operation_schema",
    "get_or_post",
    "get_properties",
    "get_schemas",
    "get_sentence_number",
    "get_submission",
    "get_word_number",
    "has_linked_sheets",
    "is_accession",
    "is_provisional",
    "is_valid_http_method",
    "label_to_api_name",
    "link_sheet",
    "lut_add",
    "merge_linked_sheet",
    "multi_lut_add",
    "na_to_empty_list",
    "new_submission",
    "parse_ega_body",
    "parse_enum",
    "parse_json_body",
    "parse_text_body",
    "process_chromosomes",
    "process_delimited_column",
    "rollback_submission",
    "row_table_formatter",
    "samples_in_db",
    "save_log",
    "step_msg",
    "submit_table",
    "try_step",
    "unbox_list",
    "unbox_row",
    "use_submission",
    "validate_schema",
    "validation_to_msg",
    "workflow_error_handler"
  ],
  "_help": [
    {
      "page": "add_required_str",
      "title": "Mark Required Fields with a Prefix",
      "topics": [
        "add_required_str"
      ]
    },
    {
      "page": "aliases_formatter",
      "title": "Format Aliases from a Table",
      "topics": [
        "aliases_formatter"
      ]
    },
    {
      "page": "api_function_factory",
      "title": "Generate an API Function from Operation and Specification",
      "topics": [
        "api_function_factory"
      ]
    },
    {
      "page": "api_name_to_label",
      "title": "Convert API Names to Prettified Labels",
      "topics": [
        "api_name_to_label"
      ]
    },
    {
      "page": "column_table_formatter",
      "title": "Format a Column Table",
      "topics": [
        "column_table_formatter"
      ]
    },
    {
      "page": "create_client",
      "title": "Generate API Client Functions",
      "topics": [
        "create_client"
      ]
    },
    {
      "page": "default_parser",
      "title": "Parser for a Default EGA Excel Template",
      "topics": [
        "default_parser"
      ]
    },
    {
      "page": "default_validator",
      "title": "Validator for Default Parser",
      "topics": [
        "default_validator"
      ]
    },
    {
      "page": "delete_submission",
      "title": "Delete a Submission and Log Responses",
      "topics": [
        "delete_submission"
      ]
    },
    {
      "page": "delete_submission_contents",
      "title": "Delete Submission Contents and Log Responses",
      "topics": [
        "delete_submission_contents"
      ]
    },
    {
      "page": "DELIM_CONVERTERS",
      "title": "Default Column Converters for EGA Metadata",
      "topics": [
        "DELIM_CONVERTERS"
      ]
    },
    {
      "page": "ega_oauth",
      "title": "Set The OAUTH With EGA Username And Password",
      "topics": [
        "ega_oauth"
      ]
    },
    {
      "page": "ega_token",
      "title": "Retrieve EGA API Bearer Token",
      "topics": [
        "ega_token"
      ]
    },
    {
      "page": "extract_api",
      "title": "Extract API Specification and Host Details",
      "topics": [
        "extract_api"
      ]
    },
    {
      "page": "extract_operation_definitions",
      "title": "Extract API Operation Definitions",
      "topics": [
        "extract_operation_definitions"
      ]
    },
    {
      "page": "extract_resource_name",
      "title": "Extract Resource Name from API Response URL",
      "topics": [
        "extract_resource_name"
      ]
    },
    {
      "page": "fetch_files",
      "title": "Fetch file information from EGA inbox",
      "topics": [
        "fetch_files"
      ]
    },
    {
      "page": "file_formatter",
      "title": "Format File Table with EGA File Paths",
      "topics": [
        "file_formatter"
      ]
    },
    {
      "page": "filter_id_fields",
      "title": "Filter Out ID Fields from a Character Vector",
      "topics": [
        "filter_id_fields"
      ]
    },
    {
      "page": "finalise_submission",
      "title": "Finalise an EGA submission",
      "topics": [
        "finalise_submission"
      ]
    },
    {
      "page": "first_row_to_colnames",
      "title": "Use First Row as Column Names for a Data Frame",
      "topics": [
        "first_row_to_colnames"
      ]
    },
    {
      "page": "fold_column",
      "title": "Fold Columns with a Common Prefix into a Single Column Nested as List",
      "topics": [
        "fold_column"
      ]
    },
    {
      "page": "format_chromosomes",
      "title": "Format Chromosome Metadata",
      "topics": [
        "format_chromosomes"
      ]
    },
    {
      "page": "get_chr_group",
      "title": "Retrieve Chromosome Belonging to a Group",
      "topics": [
        "get_chr_group"
      ]
    },
    {
      "page": "get_entry_by_title",
      "title": "Retrieve EGA entries by title",
      "topics": [
        "get_entry_by_title"
      ]
    },
    {
      "page": "get_enum",
      "title": "Retrieve Enum Values from an API",
      "topics": [
        "get_enum"
      ]
    },
    {
      "page": "get_formatter",
      "title": "Retrieve a Formatter Function by Type of Submission Metadata Table",
      "topics": [
        "get_formatter"
      ]
    },
    {
      "page": "get_formatter_params",
      "title": "Retrieve Formatter Parameters by Name",
      "topics": [
        "get_formatter_params"
      ]
    },
    {
      "page": "get_operation_schema",
      "title": "Retrieve the Schema for an API Operation",
      "topics": [
        "get_operation_schema"
      ]
    },
    {
      "page": "get_or_post",
      "title": "Retrieve or Submit Data to an EGA API Endpoint",
      "topics": [
        "get_or_post"
      ]
    },
    {
      "page": "get_properties",
      "title": "Extract and Format Properties from a Schema",
      "topics": [
        "get_properties"
      ]
    },
    {
      "page": "get_schemas",
      "title": "Retrieve Request schemas from an API Specification",
      "topics": [
        "get_schemas"
      ]
    },
    {
      "page": "get_sentence_number",
      "title": "Count the number of sentences in text",
      "topics": [
        "get_sentence_number"
      ]
    },
    {
      "page": "get_submission",
      "title": "Retrieve Submission Data and Log Responses",
      "topics": [
        "get_submission"
      ]
    },
    {
      "page": "get_word_number",
      "title": "Count the number of words in text",
      "topics": [
        "get_word_number"
      ]
    },
    {
      "page": "has_linked_sheets",
      "title": "Check for Linked Sheets in Metadata",
      "topics": [
        "has_linked_sheets"
      ]
    },
    {
      "page": "is_accession",
      "title": "Check if a String is a Valid Accession Identifier.",
      "topics": [
        "is_accession"
      ]
    },
    {
      "page": "is_provisional",
      "title": "Check whether IDs is a provisional ID.",
      "topics": [
        "is_provisional"
      ]
    },
    {
      "page": "is_valid_http_method",
      "title": "Validate HTTP Method",
      "topics": [
        "is_valid_http_method"
      ]
    },
    {
      "page": "label_to_api_name",
      "title": "Convert Prettified Labels to API Names",
      "topics": [
        "label_to_api_name"
      ]
    },
    {
      "page": "link_sheet",
      "title": "Link Data Between Metadata Sheets",
      "topics": [
        "link_sheet"
      ]
    },
    {
      "page": "lut_add",
      "title": "Add a Column to a Data Frame Based on Lookup Table",
      "topics": [
        "lut_add"
      ]
    },
    {
      "page": "merge_linked_sheet",
      "title": "Merge Linked Sheets with Source Data",
      "topics": [
        "merge_linked_sheet"
      ]
    },
    {
      "page": "multi_lut_add",
      "title": "Add Multiple Lookup-Based Columns to a Data Frame",
      "topics": [
        "multi_lut_add"
      ]
    },
    {
      "page": "na_to_empty_list",
      "title": "Convert NA Values to Empty Lists",
      "topics": [
        "na_to_empty_list"
      ]
    },
    {
      "page": "new_submission",
      "title": "Submit New Data to EGA",
      "topics": [
        "new_submission"
      ]
    },
    {
      "page": "parse_ega_body",
      "title": "Parse The Information From EGA httr2 Response Object.",
      "topics": [
        "parse_ega_body"
      ]
    },
    {
      "page": "parse_enum",
      "title": "Parse Enum into a Formatted String",
      "topics": [
        "parse_enum"
      ]
    },
    {
      "page": "parse_json_body",
      "title": "Parse and Standardize JSON Response Body",
      "topics": [
        "parse_json_body"
      ]
    },
    {
      "page": "parse_text_body",
      "title": "Parse Plain Text or JSON-like Response Body",
      "topics": [
        "parse_text_body"
      ]
    },
    {
      "page": "process_chromosomes",
      "title": "Process a Vector or List of Chromosome Data",
      "topics": [
        "process_chromosomes"
      ]
    },
    {
      "page": "process_delimited_column",
      "title": "Process Delimited Columns in Metadata",
      "topics": [
        "process_delimited_column"
      ]
    },
    {
      "page": "rollback_submission",
      "title": "Rollback Submission Endpoints and Log Responses",
      "topics": [
        "rollback_submission"
      ]
    },
    {
      "page": "row_table_formatter",
      "title": "Format a Row Table",
      "topics": [
        "row_table_formatter"
      ]
    },
    {
      "page": "samples_in_db",
      "title": "Check if sample aliases exist in the EGA database",
      "topics": [
        "samples_in_db"
      ]
    },
    {
      "page": "save_log",
      "title": "Save API Responses to a Log File",
      "topics": [
        "save_log"
      ]
    },
    {
      "page": "step_msg",
      "title": "Generate a Step-by-Step Message Function",
      "topics": [
        "step_msg"
      ]
    },
    {
      "page": "submit_table",
      "title": "Submit a Data Frame to an API Endpoint Row by Row",
      "topics": [
        "submit_table"
      ]
    },
    {
      "page": "try_step",
      "title": "Execute a submission step with error handling and rollback",
      "topics": [
        "try_step"
      ]
    },
    {
      "page": "unbox_list",
      "title": "Convert a List to an Unboxed JSON-Compatible Data Frame",
      "topics": [
        "unbox_list"
      ]
    },
    {
      "page": "unbox_row",
      "title": "Convert a Data Frame Row to an Unboxed JSON Object",
      "topics": [
        "unbox_row"
      ]
    },
    {
      "page": "use_submission",
      "title": "Retrieve or Delete Submission Data",
      "topics": [
        "use_submission"
      ]
    },
    {
      "page": "validate_schema",
      "title": "Validate a Payload Against a JSON Schema",
      "topics": [
        "validate_schema"
      ]
    },
    {
      "page": "validation_to_msg",
      "title": "Convert Validation Results to a Message",
      "topics": [
        "validation_to_msg"
      ]
    },
    {
      "page": "workflow_error_handler",
      "title": "Workflow Error Handler",
      "topics": [
        "workflow_error_handler"
      ]
    }
  ],
  "_readme": "https://github.com/bioc/Rega/raw/HEAD/README.md",
  "_rundeps": [
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    "cellranger",
    "cli",
    "cpp11",
    "crayon",
    "curl",
    "dplyr",
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    "glue",
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    "openssl",
    "pillar",
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    "rappdirs",
    "Rcpp",
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      "filename": "Rega.html",
      "title": "The Rega User Guide",
      "author": "Igor Cervenka, Athimed El Taher, Robert Ivánek",
      "engine": "knitr::rmarkdown",
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        "Load packages",
        "Setting Up Secure Credentials",
        "Using operating system credential store",
        "Using environmental variables with httr2 secret",
        "Create and Store a Master Secret Key",
        "Encrypt your EGA password",
        "Store the encrypted password",
        "Store your username",
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        "Fill in the submission template",
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