OmicsData-class         OmicsData Class
calculate_cooks_distance
                        Calculate Cook's Distance
calculate_lof           Calculate Local Outlier Factor (LOF)
calculate_measures      Calculate Measures for Each Feature
calculate_qc_rsd        Calculate QC Statistics and RSD
check_and_sort_columns
                        Check and Sort Columns, Compare Values
check_match             Check Match
combine_logical_tibbles
                        Combine Multiple Logical Tibbles with
                        Intersection or Union
convert_mrm_data        Convert MRM Data to Wide Format
convert_to_binary_matrix
                        Convert to Binary Matrix for UpSetR
createOmicsData         Constructor for OmicsData
define_thresholds       Define Anomaly Thresholds
detect_duplicates       Detect Duplicate MRM Transitions
ensure_enough_sets_for_upset
                        Ensure There Are Enough Sets for UpSet Plot
flag_anomalies          Flag Anomalies
flag_underexpressed_features
                        Flag Underexpressed Features in Samples Based
                        on Blank Samples
generate_data_with_anomalies
                        Generate High-Dimensional Data with Anomalies
generate_process_report
                        Generate Process Report for Sciex 7500/5500 Raw
                        Data
handle_missing_values   Handle Missing Values in a Tibble
initialize_results_df   Initialize Results Data Frame
internal_standard_normalize
                        Internal Standard Normalize
load_parse_sciex_txt    Load and Parse SCIEX OS Exported LC-MRM-MS2
                        Data
ms1_annotation          MS1 Annotation
perform_batch_assessment
                        Perform Principal Variance Component Analysis
                        for Batch Effect Assessment
perform_feature_selection
                        Perform Feature Selection
pieDraw                 Plot PVCA results (pie chart)
plot_distribution_measures
                        Plot Distribution Measures
plot_lipid_data_summary
                        Plot and Analyze Lipid Class Data
plot_met_data_summary   Plot and Analyze Metabolomics Data Summary
plot_sample_measures    Plot Sample Measures
pqn_normalize           Perform Probabilistic Quotient Normalization
                        for intensities
prepare_upset_data      Prepare Data for UpSet Plot
process_mrm_duplicates
                        Process All MRM Transitions for Duplicates
pvcaDraw                Plot PVCA results (bar chart)
qc_normalize            QC-RLSC Normalize function
run_app                 Run the Shiny Application
transpose_df            Transpose DataFrame
