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  "Description": "This package contains utility functions used throughout\nthe gDR platform to fit data, manipulate data, and convert and\nvalidate data structures. This package also has the necessary\ndefault constants for gDR platform. Many of the functions are\nutilized by the gDRcore package.",
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    },
    {
      "page": "get_additional_variables",
      "title": "Identify and return additional variables in list of dt",
      "topics": [
        "get_additional_variables"
      ]
    },
    {
      "page": "get_assay_dt_duplicated_rows",
      "title": "Helper function to find duplicated rows in assay data",
      "topics": [
        "get_assay_dt_duplicated_rows"
      ]
    },
    {
      "page": "get_assay_names",
      "title": "get assay names of the given se/dataset fetch the data from the se if provided as metadata use predefined values from 'get_env_assay_names' otherwise",
      "topics": [
        "get_assay_names"
      ]
    },
    {
      "page": "get_assay_req_uniq_cols",
      "title": "get columns in the assay data required to have unique data",
      "topics": [
        "get_assay_req_uniq_cols"
      ]
    },
    {
      "page": "get_combo_assay_names",
      "title": "get names of combo assays",
      "topics": [
        "get_combo_assay_names"
      ]
    },
    {
      "page": "get_combo_base_assay_names",
      "title": "get names of combo base assays",
      "topics": [
        "get_combo_base_assay_names"
      ]
    },
    {
      "page": "get_combo_excess_field_names",
      "title": "get names of combo excess fields",
      "topics": [
        "get_combo_excess_field_names"
      ]
    },
    {
      "page": "get_combo_score_assay_names",
      "title": "get names of combo score assays",
      "topics": [
        "get_combo_score_assay_names"
      ]
    },
    {
      "page": "get_combo_score_field_names",
      "title": "get names of combo score fields",
      "topics": [
        "get_combo_score_field_names"
      ]
    },
    {
      "page": "get_default_identifiers",
      "title": "Get gDR default identifiers required for downstream analysis.",
      "topics": [
        "get_default_identifiers"
      ]
    },
    {
      "page": "get_duplicated_rows",
      "title": "Helper function to find duplicated rows",
      "topics": [
        "get_duplicated_rows"
      ]
    },
    {
      "page": "get_env_assay_names",
      "title": "get default assay names for the specified filters, i.e. set of assay types, assay groups and assay data types",
      "topics": [
        "get_env_assay_names"
      ]
    },
    {
      "page": "get_env_var",
      "title": "safe wrapper of Sys.getenv()",
      "topics": [
        "get_env_var"
      ]
    },
    {
      "page": "get_expect_one_identifiers",
      "title": "Get identifiers that expect only one value for each identifier.",
      "topics": [
        "get_expect_one_identifiers"
      ]
    },
    {
      "page": "get_experiment_groups",
      "title": "get_experiment_groups",
      "topics": [
        "get_experiment_groups"
      ]
    },
    {
      "page": "get_gDR_session_info",
      "title": "get gDR package and their version installed in the environment",
      "topics": [
        "get_gDR_session_info"
      ]
    },
    {
      "page": "get_identifiers_dt",
      "title": "Get descriptions for identifiers",
      "topics": [
        "get_identifiers_dt"
      ]
    },
    {
      "page": "get_idfs_synonyms",
      "title": "Get gDR synonyms for the identifiers",
      "topics": [
        "get_idfs_synonyms"
      ]
    },
    {
      "page": "get_isobologram_columns",
      "title": "Get isobologram column names",
      "topics": [
        "get_isobologram_columns"
      ]
    },
    {
      "page": "get_MAE_identifiers",
      "title": "get_MAE_identifiers",
      "topics": [
        "get_MAE_identifiers"
      ]
    },
    {
      "page": "get_non_empty_assays",
      "title": "get_non_empty_assays",
      "topics": [
        "get_non_empty_assays"
      ]
    },
    {
      "page": "get_optional_coldata_fields",
      "title": "get optional colData fields",
      "topics": [
        "get_optional_coldata_fields"
      ]
    },
    {
      "page": "get_optional_rowdata_fields",
      "title": "get optional rowData fields",
      "topics": [
        "get_optional_rowdata_fields"
      ]
    },
    {
      "page": "get_required_identifiers",
      "title": "Get identifiers required for downstream analysis.",
      "topics": [
        "get_required_identifiers"
      ]
    },
    {
      "page": "get_settings_from_json",
      "title": "Get settings from JSON file In most common scenario the settings are stored in JSON file to avoid hardcoding",
      "topics": [
        "get_settings_from_json"
      ]
    },
    {
      "page": "get_supported_experiments",
      "title": "get_supported_experiments",
      "topics": [
        "get_supported_experiments"
      ]
    },
    {
      "page": "get_synthetic_data",
      "title": "Get synthetic data from gDRtestData package",
      "topics": [
        "get_synthetic_data"
      ]
    },
    {
      "page": "get_testdata",
      "title": "get_testdata",
      "topics": [
        "get_testdata"
      ]
    },
    {
      "page": "get_testdata_codilution",
      "title": "get_testdata_codilution",
      "topics": [
        "get_testdata_codilution"
      ]
    },
    {
      "page": "get_testdata_combo",
      "title": "get_testdata_combo",
      "topics": [
        "get_testdata_combo"
      ]
    },
    {
      "page": "has_assay_dt_duplicated_rows",
      "title": "check if assay data contains duplicated data",
      "topics": [
        "has_assay_dt_duplicated_rows"
      ]
    },
    {
      "page": "has_dt_duplicated_rows",
      "title": "check if data.table contains duplicated data",
      "topics": [
        "has_dt_duplicated_rows"
      ]
    },
    {
      "page": "has_single_codrug_data",
      "title": "Has Single Codrug Data",
      "topics": [
        "has_single_codrug_data"
      ]
    },
    {
      "page": "has_valid_codrug_data",
      "title": "Has Valid Codrug Data",
      "topics": [
        "has_valid_codrug_data"
      ]
    },
    {
      "page": "headers",
      "title": "Get or reset headers for one or all header field(s) respectively",
      "topics": [
        "get_header",
        "headers"
      ]
    },
    {
      "page": "identifiers",
      "title": "Get, set, or reset identifiers for one or all identifier field(s)",
      "topics": [
        "get_env_identifiers",
        "get_prettified_identifiers",
        "identifiers",
        "reset_env_identifiers",
        "set_env_identifier"
      ]
    },
    {
      "page": "identify_unique_se_metadata_fields",
      "title": "Identify unique metadata fields from a list of 'SummarizedExperiment's",
      "topics": [
        "identify_unique_se_metadata_fields"
      ]
    },
    {
      "page": "is_any_exp_empty",
      "title": "is_any_exp_empty",
      "topics": [
        "is_any_exp_empty"
      ]
    },
    {
      "page": "is_combo_data",
      "title": "Checks if 'se' is combo dataset.",
      "topics": [
        "is_combo_data"
      ]
    },
    {
      "page": "is_exp_empty",
      "title": "is_exp_empty",
      "topics": [
        "is_exp_empty"
      ]
    },
    {
      "page": "is_mae_empty",
      "title": "is_mae_empty",
      "topics": [
        "is_mae_empty"
      ]
    },
    {
      "page": "logisticFit",
      "title": "Logistic fit",
      "topics": [
        "logisticFit"
      ]
    },
    {
      "page": "loop",
      "title": "Conditional lapply or bplapply with optional batch processing.",
      "topics": [
        "loop"
      ]
    },
    {
      "page": "MAEpply",
      "title": "Lapply through all the experiments in MultiAssayExperiment object",
      "topics": [
        "MAEpply"
      ]
    },
    {
      "page": "map_conc_to_standardized_conc",
      "title": "Create a mapping of concentrations to standardized concentrations.",
      "topics": [
        "map_conc_to_standardized_conc"
      ]
    },
    {
      "page": "mcolData",
      "title": "mcolData",
      "topics": [
        "mcolData"
      ]
    },
    {
      "page": "merge_assay",
      "title": "Merge assay data",
      "topics": [
        "merge_assay"
      ]
    },
    {
      "page": "merge_MAE",
      "title": "Merge multiple MultiAssayExperiment objects",
      "topics": [
        "merge_MAE"
      ]
    },
    {
      "page": "merge_metadata",
      "title": "Merge metadata",
      "topics": [
        "merge_metadata"
      ]
    },
    {
      "page": "merge_SE",
      "title": "Merge multiple Summarized Experiments",
      "topics": [
        "merge_SE"
      ]
    },
    {
      "page": "modifyData",
      "title": "modify assay with additional data",
      "topics": [
        "modifyData",
        "modifyData.data_source",
        "modifyData.default",
        "modifyData.drug_name2"
      ]
    },
    {
      "page": "mrowData",
      "title": "mrowData",
      "topics": [
        "mrowData"
      ]
    },
    {
      "page": "predict_conc_from_efficacy",
      "title": "Predict a concentration for a given efficacy with fit parameters.",
      "topics": [
        "predict_conc_from_efficacy"
      ]
    },
    {
      "page": "predict_efficacy_from_conc",
      "title": "Predict efficacy values given fit parameters and a concentration.",
      "topics": [
        "predict_efficacy_from_conc"
      ]
    },
    {
      "page": "predict_smooth_from_combo",
      "title": "Predict a smoothed response for a drug combination",
      "topics": [
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      ]
    },
    {
      "page": "prettify_flat_metrics",
      "title": "Prettify metric names in flat 'Metrics' assay",
      "topics": [
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    },
    {
      "page": "process_batch",
      "title": "Process and save a batch of results.",
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    {
      "page": "promote_fields",
      "title": "Promote a nested field to be represented as a metadata field of the 'SummarizedExperiment' as either the 'rowData' or 'colData'.",
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    },
    {
      "page": "refine_coldata",
      "title": "refine colData",
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    {
      "page": "refine_rowdata",
      "title": "refine rowData",
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      "title": "Remove Codrug Data",
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      "page": "remove_drug_batch",
      "title": "Remove batch substring from drug id",
      "topics": [
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      "page": "rename_bumpy",
      "title": "Rename BumpyMatrix",
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      "title": "Rename DFrame",
      "topics": [
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      "page": "round_concentration",
      "title": "Round concentration to ndigit significant digits",
      "topics": [
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      "page": "SE_metadata",
      "title": "Get and set metadata for parameters on a SummarizedExperiment object.",
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        "get_SE_fit_parameters",
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        "SE_metadata"
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      "title": "Set fit parameters for a constant fit.",
      "topics": [
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    },
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      "page": "set_unique_cl_names",
      "title": "Set Unique Parental Identifiers",
      "topics": [
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      ]
    },
    {
      "page": "set_unique_cl_names_dt",
      "title": "Set unique primary cell line identifiers in the table",
      "topics": [
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    },
    {
      "page": "set_unique_drug_names",
      "title": "Set Unique Drug Names",
      "topics": [
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    },
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      "page": "set_unique_drug_names_dt",
      "title": "Set unique primary drug identifiers in the table",
      "topics": [
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    {
      "page": "set_unique_identifiers",
      "title": "Set Unique Identifiers in MultiAssayExperiment",
      "topics": [
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      "title": "Set unique primary identifiers in the data.frame-like objects",
      "topics": [
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    {
      "page": "shorten_normalization_type_name",
      "title": "shorten normalization type",
      "topics": [
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      ]
    },
    {
      "page": "split_big_table_for_xlsx",
      "title": "Split big table",
      "topics": [
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      "page": "split_SE_components",
      "title": "split_SE_components",
      "topics": [
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      "title": "Standardize MAE by switching from custom identifiers into gDR-default",
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      "title": "Standardize SE by switching from custom identifiers into gDR-default",
      "topics": [
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      "title": "Validate SummarizedExperiment object",
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      "title": "Check whether or not an assay exists in a SummarizedExperiment object.",
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