.set_invalid_fit_params
                        Set fit parameters for an invalid fit.
.standardize_conc       Standardize concentration values.
MAEpply                 Lapply through all the experiments in
                        MultiAssayExperiment object
SE_metadata             Get and set metadata for parameters on a
                        SummarizedExperiment object.
addClass                add arbitrary S3 class to an object
aggregate_assay         Aggregate a 'BumpyMatrix' assay by a given
                        aggregation function.
apply_bumpy_function    Apply a function to every element of a bumpy
                        matrix.
assert_choices          assert choices
average_biological_replicates_dt
                        Average biological replicates on the data table
                        side.
calc_sd                 Calculate Standard Deviation or Return Zero
cap_assay_infinities    Cap infinity values (Inf, -Inf) in the assay
                        data
cap_xc50                Cap XC50 value.
convert_colData_to_json
                        Convert colData to JSON
convert_combo_data_to_dt
                        convert combo assays from SummarizedExperiments
                        to the list of data.tables
convert_combo_field_to_assay
                        get combo assay names based on the field name
convert_mae_assay_to_dt
                        Convert a MultiAssayExperiment assay to a long
                        data.table
convert_mae_to_json     Create JSON document.
convert_metadata_to_json
                        Convert experiment metadata to JSON format for
                        elasticsearch indexing.
convert_rowData_to_json
                        Convert rowData to JSON
convert_se_assay_to_custom_dt
                        Convert a SummarizedExperiment assay to a long
                        data.table and conduct some post processing
                        steps
convert_se_assay_to_dt
                        Convert a SummarizedExperiment assay to a long
                        data.table
convert_se_to_json      Convert a SummarizedExperiment object to a JSON
                        document.
define_matrix_grid_positions
                        Define matrix grid positions
demote_fields           Demote a metadata field in the 'rowData' or
                        'colData' of a 'SummarizedExperiment' object to
                        a nested field of a 'BumpyMatrix' assay.
df_to_bm_assay          df_to_bm_assay
extend_normalization_type_name
                        extend abbreviated normalization type
fit_curves              Fit curves
flatten                 Flatten a table
gen_synthetic_data      gen_synthetic_data
get_MAE_identifiers     get_MAE_identifiers
get_additional_variables
                        Identify and return additional variables in
                        list of dt
get_assay_dt_duplicated_rows
                        Helper function to find duplicated rows in
                        assay data
get_assay_names         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
get_assay_req_uniq_cols
                        get columns in the assay data required to have
                        unique data
get_combo_assay_names   get names of combo assays
get_combo_base_assay_names
                        get names of combo base assays
get_combo_excess_field_names
                        get names of combo excess fields
get_combo_score_assay_names
                        get names of combo score assays
get_combo_score_field_names
                        get names of combo score fields
get_default_identifiers
                        Get gDR default identifiers required for
                        downstream analysis.
get_duplicated_rows     Helper function to find duplicated rows
get_env_assay_names     get default assay names for the specified
                        filters, i.e. set of assay types, assay groups
                        and assay data types
get_env_var             safe wrapper of Sys.getenv()
get_expect_one_identifiers
                        Get identifiers that expect only one value for
                        each identifier.
get_experiment_groups   get_experiment_groups
get_gDR_session_info    get gDR package and their version installed in
                        the environment
get_identifiers_dt      Get descriptions for identifiers
get_idfs_synonyms       Get gDR synonyms for the identifiers
get_isobologram_columns
                        Get isobologram column names
get_non_empty_assays    get_non_empty_assays
get_optional_coldata_fields
                        get optional colData fields
get_optional_rowdata_fields
                        get optional rowData fields
get_required_identifiers
                        Get identifiers required for downstream
                        analysis.
get_settings_from_json
                        Get settings from JSON file In most common
                        scenario the settings are stored in JSON file
                        to avoid hardcoding
get_supported_experiments
                        get_supported_experiments
get_synthetic_data      Get synthetic data from gDRtestData package
get_testdata            get_testdata
get_testdata_codilution
                        get_testdata_codilution
get_testdata_combo      get_testdata_combo
has_assay_dt_duplicated_rows
                        check if assay data contains duplicated data
has_dt_duplicated_rows
                        check if data.table contains duplicated data
has_single_codrug_data
                        Has Single Codrug Data
has_valid_codrug_data   Has Valid Codrug Data
headers                 Get or reset headers for one or all header
                        field(s) respectively
identifiers             Get, set, or reset identifiers for one or all
                        identifier field(s)
identify_unique_se_metadata_fields
                        Identify unique metadata fields from a list of
                        'SummarizedExperiment's
is_any_exp_empty        is_any_exp_empty
is_combo_data           Checks if 'se' is combo dataset.
is_exp_empty            is_exp_empty
is_mae_empty            is_mae_empty
logisticFit             Logistic fit
loop                    Conditional lapply or bplapply with optional
                        batch processing.
map_conc_to_standardized_conc
                        Create a mapping of concentrations to
                        standardized concentrations.
mcolData                mcolData
merge_MAE               Merge multiple MultiAssayExperiment objects
merge_SE                Merge multiple Summarized Experiments
merge_assay             Merge assay data
merge_metadata          Merge metadata
modifyData              modify assay with additional data
mrowData                mrowData
predict_conc_from_efficacy
                        Predict a concentration for a given efficacy
                        with fit parameters.
predict_efficacy_from_conc
                        Predict efficacy values given fit parameters
                        and a concentration.
predict_smooth_from_combo
                        Predict a smoothed response for a drug
                        combination
prettify_flat_metrics   Prettify metric names in flat 'Metrics' assay
process_batch           Process and save a batch of results.
promote_fields          Promote a nested field to be represented as a
                        metadata field of the 'SummarizedExperiment' as
                        either the 'rowData' or 'colData'.
refine_coldata          refine colData
refine_rowdata          refine rowData
remove_codrug_data      Remove Codrug Data
remove_drug_batch       Remove batch substring from drug id
rename_DFrame           Rename DFrame
rename_bumpy            Rename BumpyMatrix
round_concentration     Round concentration to ndigit significant
                        digits
set_constant_fit_params
                        Set fit parameters for a constant fit.
set_unique_cl_names     Set Unique Parental Identifiers
set_unique_cl_names_dt
                        Set unique primary cell line identifiers in the
                        table
set_unique_drug_names   Set Unique Drug Names
set_unique_drug_names_dt
                        Set unique primary drug identifiers in the
                        table
set_unique_identifiers
                        Set Unique Identifiers in MultiAssayExperiment
set_unique_names_dt     Set unique primary identifiers in the
                        data.frame-like objects
shorten_normalization_type_name
                        shorten normalization type
split_SE_components     split_SE_components
split_big_table_for_xlsx
                        Split big table
standardize_mae         Standardize MAE by switching from custom
                        identifiers into gDR-default
standardize_se          Standardize SE by switching from custom
                        identifiers into gDR-default
strip_first_and_last_char
                        String first and last characters of a string.
throw_msg_if_duplicates
                        throw message if assay data.table contains
                        duplicated rows
update_env_idfs_from_mae
                        Update environment identifiers from MAE object
                        identifiers
update_idfs_synonyms    Update gDR synonyms for the identifier
validate_MAE            Validate MultiAssayExperiment object
validate_SE             Validate SummarizedExperiment object
validate_dimnames       Validate dimnames
validate_identifiers    Check that specified identifier values exist in
                        the data.
validate_json           Validate JSON against a schema.
validate_mae_with_schema
                        Validate MAE against a schema.
validate_se_assay_name
                        Check whether or not an assay exists in a
                        SummarizedExperiment object.
