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  "Title": "Processing functions and interface to process and analyze drug\ndose-response data",
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  "Description": "This package contains core functions to process and\nanalyze drug response data. The package provides tools for\nnormalizing, averaging, and calculation of gDR metrics data.\nAll core functions are wrapped into the pipeline function\nallowing analyzing the data in a straightforward way.",
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  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-05-28 12:17:11 UTC",
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  "Author": "Bartosz Czech [aut] (ORCID: <https://orcid.org/0000-0002-9908-3007>),\nArkadiusz Gladki [cre, aut] (ORCID:\n<https://orcid.org/0000-0002-7059-6378>),\nMarc Hafner [aut] (ORCID: <https://orcid.org/0000-0003-1337-7598>),\nPawel Piatkowski [aut],\nNatalia Potocka [aut],\nDariusz Scigocki [aut],\nJanina Smola [aut],\nSergiu Mocanu [aut],\nMarcin Kamianowski [aut],\nAllison Vuong [aut]",
  "Maintainer": "Arkadiusz Gladki <gladki.arkadiusz@gmail.com>",
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    "annotate_se_with_cell_line",
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    "calculate_excess",
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    "cleanup_metadata",
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    "get_drug_annotation",
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    "identify_data_type",
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    "merge_data",
    "normalize_SE",
    "prepare_input",
    "process_perturbations",
    "replace_conc_with_standardized_conc",
    "runDrugResponseProcessingPipeline",
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    "test_synthetic_data"
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      "title": "annotate_dt_with_cell_line",
      "topics": [
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    },
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      "page": "annotate_dt_with_drug",
      "title": "annotate_dt_with_drug",
      "topics": [
        "annotate_dt_with_drug"
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    },
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      "title": "annotate_mae_with_cell_line",
      "topics": [
        "annotate_mae_with_cell_line"
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    },
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      "page": "annotate_mae_with_drug",
      "title": "annotate_mae_with_drug",
      "topics": [
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      "title": "annotate_se_with_cell_line",
      "topics": [
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    },
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      "page": "annotate_se_with_drug",
      "title": "annotate_se_with_drug",
      "topics": [
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      "title": "Run drug response processing pipeline",
      "topics": [
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        "create_and_normalize_SE",
        "create_SE",
        "fit_SE",
        "normalize_SE",
        "runDrugResponseProcessingPipeline",
        "runDrugResponseProcessingPipelineFxns"
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      "topics": [
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        "calculate_GR_value",
        "calculate_time_dep_GR_value"
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    },
    {
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      "title": "Calculate a metric for combination data.",
      "topics": [
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        "calculate_Bliss",
        "calculate_HSA",
        "calculate_matrix_metric"
      ]
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      "title": "Calculate score for HSA and Bliss",
      "topics": [
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      "page": "cleanup_metadata",
      "title": "cleanup_metadata",
      "topics": [
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      ]
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      "title": "Transform se into raw_data",
      "topics": [
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    },
    {
      "page": "data_model",
      "title": "Detect model of data",
      "topics": [
        "data_model"
      ]
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      "page": "data_model.character",
      "title": "Detect model of data from experiment name",
      "topics": [
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      "title": "Detect model of data in data.table",
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      "title": "fit_SE for combination screens",
      "topics": [
        "fit_SE.combinations"
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    },
    {
      "page": "get_assays_per_pipeline_step",
      "title": "get info about created/present assays in SE at the given pipeline step",
      "topics": [
        "get_assays_per_pipeline_step"
      ]
    },
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      "page": "get_cell_line_annotation",
      "title": "get_cell_line_annotation",
      "topics": [
        "get_cell_line_annotation"
      ]
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    {
      "page": "get_cellline_annotation_from_dt",
      "title": "Retrieve the cell line annotation from the annotated dt input",
      "topics": [
        "get_cellline_annotation_from_dt"
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    },
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        "get_default_nested_identifiers.data.table",
        "get_default_nested_identifiers.SummarizedExperiment"
      ]
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      "title": "get_drug_annotation",
      "topics": [
        "get_drug_annotation"
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      "page": "get_drug_annotation_from_dt",
      "title": "Retrieve the drug annotation from the annotated dt input",
      "topics": [
        "get_drug_annotation_from_dt"
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      "title": "Value Matching",
      "topics": [
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      "topics": [
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      "topics": [
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      "title": "Identify untreated rows based on Drug treatment alone",
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