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  "Package": "SerolyzeR",
  "Type": "Package",
  "Title": "Reading, Quality Control and Preprocessing of MBA (Multiplex\nBead Assay) Data",
  "Description": "Speeds up the process of loading raw data from MBA\n(Multiplex Bead Assay) examinations, performs quality control\nchecks, and automatically normalises the data, preparing it for\nmore advanced, downstream tasks. The main objective of the\npackage is to create a simple environment for a user, who does\nnot necessarily have experience with R language. The package is\ndeveloped within the project 'PvSTATEM', which is an\ninternational project aiming for malaria elimination.",
  "BugReports": "https://github.com/mini-pw/SerolyzeR/issues",
  "Version": "1.4.1",
  "License": "BSD_3_clause + file LICENSE",
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  "Authors@R": "c(\nperson(\"Jakub\", \"Grzywaczewski\", email = \"jakubzgrzywaczewski@gmail.com\", role = c(\"aut\", \"cre\")),\nperson(\"Tymoteusz\", \"Kwiecinski\", email = \"tymoteuszkwiecinski@gmail.com\", role = c(\"aut\"),\ncomment = c(ORCID = \"0009-0006-7362-9821\")),\nperson(\"Mateusz\", \"Nizwantowski\", email = \"mateusznizwantowski@gmail.com\", role = c(\"aut\")),\nperson(\"Przemyslaw\", \"Biecek\", email = \"przemyslaw.biecek@gmail.com\", role = c(\"ths\"),\ncomment = c(ORCID = \"0000-0001-8423-1823\")),\nperson(\"Nuno\", \"Sepulveda\", email = \"nuno.sepulveda@pw.edu.pl\", role = c(\"ths\"),\ncomment = c(ORCID = \"0000-0002-8542-1706\")))",
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  "URL": "https://github.com/mini-pw/SerolyzeR,\nhttps://mini-pw.github.io/SerolyzeR/",
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  "Repository": "https://mini-pw.r-universe.dev",
  "Date/Publication": "2026-02-19 15:11:51 UTC",
  "RemoteUrl": "https://github.com/mini-pw/serolyzer",
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  "NeedsCompilation": "no",
  "Packaged": {
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    "User": "root"
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  "Author": "Jakub Grzywaczewski [aut, cre],\nTymoteusz Kwiecinski [aut] (ORCID:\n<https://orcid.org/0009-0006-7362-9821>),\nMateusz Nizwantowski [aut],\nPrzemyslaw Biecek [ths] (ORCID:\n<https://orcid.org/0000-0001-8423-1823>),\nNuno Sepulveda [ths] (ORCID: <https://orcid.org/0000-0002-8542-1706>)",
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    "description": "Data Science MSc student at WUT.\nResearch software engineer at CCAI .\n",
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    "generate_levey_jennings_report",
    "generate_plate_report",
    "get_nmfi",
    "is_valid_data_type",
    "is_valid_sample_type",
    "merge_plate_outputs",
    "PlateBuilder",
    "plot_counts",
    "plot_layout",
    "plot_levey_jennings",
    "plot_mfi_for_analyte",
    "plot_standard_curve_analyte",
    "plot_standard_curve_analyte_with_model",
    "plot_standard_curve_stacked",
    "process_dir",
    "process_file",
    "process_plate",
    "read_layout_data",
    "read_luminex_data",
    "read_xponent_format",
    "translate_sample_names_to_sample_types"
  ],
  "_help": [
    {
      "page": "create_standard_curve_model_analyte",
      "title": "Create a standard curve model for a certain analyte",
      "topics": [
        "create_standard_curve_model_analyte"
      ]
    },
    {
      "page": "generate_levey_jennings_report",
      "title": "Generate a Levey-Jennings Report for Multiple Plates.",
      "topics": [
        "generate_levey_jennings_report"
      ]
    },
    {
      "page": "generate_plate_report",
      "title": "Generate a report for a plate.",
      "topics": [
        "generate_plate_report"
      ]
    },
    {
      "page": "get_nmfi",
      "title": "Calculate Normalised MFI (nMFI) Values for a Plate",
      "topics": [
        "get_nmfi"
      ]
    },
    {
      "page": "handle_high_dose_hook",
      "title": "Detect and handle the high dose hook effect",
      "topics": [
        "handle_high_dose_hook"
      ]
    },
    {
      "page": "is_valid_data_type",
      "title": "Check validity of given data type",
      "topics": [
        "is_valid_data_type"
      ]
    },
    {
      "page": "is_valid_sample_type",
      "title": "Check validity of given sample type",
      "topics": [
        "is_valid_sample_type"
      ]
    },
    {
      "page": "merge_plate_outputs",
      "title": "Merge Normalised Data from Multiple Plates",
      "topics": [
        "merge_plate_outputs"
      ]
    },
    {
      "page": "Model",
      "title": "Logistic regression model for the standard curve",
      "topics": [
        "Model"
      ]
    },
    {
      "page": "Plate",
      "title": "Plate Object",
      "topics": [
        "Plate"
      ]
    },
    {
      "page": "PlateBuilder",
      "title": "PlateBuilder",
      "topics": [
        "PlateBuilder"
      ]
    },
    {
      "page": "plot_counts",
      "title": "Plot counts in a 96-well plate",
      "topics": [
        "plot_counts"
      ]
    },
    {
      "page": "plot_layout",
      "title": "Plot layout of a 96-well plate",
      "topics": [
        "plot_layout"
      ]
    },
    {
      "page": "plot_levey_jennings",
      "title": "Plot Levey-Jennings chart",
      "topics": [
        "plot_levey_jennings"
      ]
    },
    {
      "page": "plot_mfi_for_analyte",
      "title": "Plot MFI value distribution for a given analyte",
      "topics": [
        "plot_mfi_for_analyte"
      ]
    },
    {
      "page": "plot_standard_curve_analyte",
      "title": "Standard curves",
      "topics": [
        "plot_standard_curve_analyte"
      ]
    },
    {
      "page": "plot_standard_curve_analyte_with_model",
      "title": "Plot standard curve of a certain analyte with fitted model",
      "topics": [
        "plot_standard_curve_analyte_with_model"
      ]
    },
    {
      "page": "plot_standard_curve_stacked",
      "title": "Standard curve stacked plot for levey-jennings report",
      "topics": [
        "plot_standard_curve_stacked"
      ]
    },
    {
      "page": "predict.Model",
      "title": "Predict the RAU values from the MFI values",
      "topics": [
        "predict.Model"
      ]
    },
    {
      "page": "process_dir",
      "title": "Process a Directory of Luminex Data Files",
      "topics": [
        "process_dir"
      ]
    },
    {
      "page": "process_file",
      "title": "Process a File to Generate Normalised Data and Reports",
      "topics": [
        "process_file"
      ]
    },
    {
      "page": "process_plate",
      "title": "Process Plate Data and Save Normalised Output",
      "topics": [
        "process_plate"
      ]
    },
    {
      "page": "read_bioplex_format",
      "title": "Read the BIOPLEX format data",
      "topics": [
        "read_bioplex_format"
      ]
    },
    {
      "page": "read_intelliflex_format",
      "title": "Read the Intelliflex format data",
      "topics": [
        "read_intelliflex_format"
      ]
    },
    {
      "page": "read_layout_data",
      "title": "Read layout data from a file",
      "topics": [
        "read_layout_data"
      ]
    },
    {
      "page": "read_luminex_data",
      "title": "Read Luminex Data",
      "topics": [
        "read_luminex_data"
      ]
    },
    {
      "page": "read_xponent_format",
      "title": "Read the xPONENT format data",
      "topics": [
        "read_xponent_format"
      ]
    },
    {
      "page": "translate_sample_names_to_sample_types",
      "title": "Translate sample names to sample types",
      "topics": [
        "translate_sample_names_to_sample_types"
      ]
    }
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      "filename": "example_script.html",
      "title": "Basic SerolyzeR functionalities",
      "author": "Tymoteusz Kwieciński",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Reading the plate object",
        "Processing the whole plate",
        "Quality control and normalisation details",
        "Plate summary and details",
        "Quality control",
        "Normalisation",
        "RAU vs dilution",
        "Inner nplr model",
        "Predicting RAU",
        "Usage",
        "nMFI"
      ],
      "created": "2024-07-08 18:16:20",
      "modified": "2026-01-17 18:24:04",
      "commits": 33
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      "filename": "multiplate_tutorial.html",
      "title": "Multiplate SerolyzeR functionalities",
      "author": "Tymoteusz Kwieciński",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "Reading the data",
        "Reading a whole directory"
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      "created": "2025-03-16 00:07:53",
      "modified": "2026-01-17 18:24:04",
      "commits": 8
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      "filename": "our_datasets.html",
      "title": "Our datasets",
      "author": "Tymoteusz Kwieciński",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "How to access the files",
        "Description of the datasets",
        "Artificial datasets",
        "Public datasets",
        "External datasets"
      ],
      "created": "2024-07-17 12:32:04",
      "modified": "2026-01-17 18:24:04",
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      "author": "Jakub Grzywaczewski",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "Basic data loading",
        "SerolyzeR as an MBA data reader"
      ],
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      "modified": "2026-01-17 18:24:04",
      "commits": 3
    },
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      "filename": "our_reports.html",
      "title": "SerolyzeR HTML reports",
      "author": "Mateusz Nizwantowski",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "Plate summary report",
        "Generating the report",
        "Warnings",
        "Additional parameters",
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      "created": "2025-01-03 09:36:17",
      "modified": "2025-07-16 19:54:53",
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    },
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      "filename": "our_plots.html",
      "title": "SerolyzeR plots",
      "author": "Mateusz Nizwantowski",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "Plate layout",
        "Counts for a given analyte",
        "Distribution of MFI values",
        "Standard curve plots",
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        "Standard curve plot with model",
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