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  "Title": "Small Molecule Mass Spectrometry Data Processing, Quality\nControl, and Reporting",
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  "Authors@R": "c(person(given = \"Bo\", family = \"Burla\", role = c(\"aut\", \"cre\"),\nemail = \"bo.burla@nus.edu.sg\", comment = c(ORCID = \"0000-0002-5918-3249\")),\nperson(given = \"Guo Shou\", family = \"Teo\", role = \"aut\",\nemail = \"guoshou@nus.edu.sg\", comment = c(ORCID = \"0000-0003-3891-1494\")),\nperson(given = \"Hyungwon\", family = \"Choi\", role = \"aut\",\nemail = \"hyung_won_choi@nus.edu.sg\", comment = c(ORCID = \"0000-0002-6687-3088\"))\n)",
  "Description": "MRMhub-QUANT, the quantitation and reporting module of the\nMRMhub toolchain, is a tool for processing, quality control,\nand visualization of targeted metabolomics and lipidomics mass\nspectrometry data.",
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  "URL": "https://github.com/SLINGhub/MRMhub,\nhttps://slinghub.github.io/MRMhub/quant/",
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  "Repository": "https://slinghub.r-universe.dev",
  "Date/Publication": "2026-10-12 02:44:51 UTC",
  "RemoteUrl": "https://github.com/SLINGhub/MRMhub",
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    "get_batch_boundaries",
    "get_calibration_metrics",
    "get_feature_count",
    "get_featurelist",
    "get_iqr_tails",
    "get_mad_tails",
    "get_outlier_bounds",
    "get_qc_bias_variability",
    "get_response_curve_stats",
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    "import_data_mztab",
    "import_data_skyline",
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    "import_metadata_features",
    "import_metadata_from_data",
    "import_metadata_istds",
    "import_metadata_msorganiser",
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    "import_metadata_responsecurves",
    "licar_pattern_choices",
    "mrmhub_enable_cli_color",
    "mrmhub_get_plot_defaults",
    "mrmhub_reset_plot_defaults",
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    "plot_qc_summary_byclass",
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    "quantify_by_istd",
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    "save_dataset_rds",
    "save_dataset_summarizedexperiment",
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    "save_metadata_templates",
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    "set_analysis_order",
    "set_intensity_var",
    "set_lipid_class",
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      "class": [
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      "table": false,
      "tojson": false
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      "title": "Access slots of a 'MRMhubExperiment' object via $ syntax",
      "topics": [
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    },
    {
      "page": "add_metadata",
      "title": "Add metadata to an 'MRMhubExperiment' object",
      "topics": [
        "add_metadata"
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    },
    {
      "page": "build_workflow",
      "title": "Launch the MRMhub Workflow Builder",
      "topics": [
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    },
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      "page": "calc_average_molweight",
      "title": "Calculate average molecular weight from chemical formulas",
      "topics": [
        "calc_average_molweight"
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    },
    {
      "page": "calc_calibration_results",
      "title": "Calculate external calibration curve results",
      "topics": [
        "calc_calibration_results"
      ]
    },
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      "page": "calc_isotopic_interferences",
      "title": "Derive isotopic interference relationships",
      "topics": [
        "calc_isotopic_interferences"
      ]
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    {
      "page": "calc_qc_metrics",
      "title": "Calculate quality control (QC) metrics for features",
      "topics": [
        "calc_qc_metrics"
      ]
    },
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      "title": "Calibrate feature values using a reference sample",
      "topics": [
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    {
      "page": "check_setup",
      "title": "Check MRMhub setup",
      "topics": [
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      "title": "Batch centering correction",
      "topics": [
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      "title": "ComBat batch correction",
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    },
    {
      "page": "correct_batch_serrf",
      "title": "SERRF batch correction",
      "topics": [
        "correct_batch_serrf"
      ]
    },
    {
      "page": "correct_custom_interferences",
      "title": "Correct declared (custom) interferences",
      "topics": [
        "correct_custom_interferences"
      ]
    },
    {
      "page": "correct_drift",
      "title": "Drift correction by custom function",
      "topics": [
        "correct_drift"
      ]
    },
    {
      "page": "correct_drift_cubicspline",
      "title": "Drift correction by cubic spline smoothing",
      "topics": [
        "correct_drift_cubicspline"
      ]
    },
    {
      "page": "correct_drift_gam",
      "title": "Drift correction by generalized additive model (GAM) smoothing",
      "topics": [
        "correct_drift_gam"
      ]
    },
    {
      "page": "correct_drift_gaussiankernel",
      "title": "Drift correction by Gaussian kernel smoothing",
      "topics": [
        "correct_drift_gaussiankernel"
      ]
    },
    {
      "page": "correct_drift_loess",
      "title": "Drift correction by LOESS smoothing",
      "topics": [
        "correct_drift_loess"
      ]
    },
    {
      "page": "correct_interference_manual",
      "title": "Manual isotopic interference correction",
      "topics": [
        "correct_interference_manual"
      ]
    },
    {
      "page": "correct_isotopic_interferences",
      "title": "Correct automatically derived isotopic interferences",
      "topics": [
        "correct_isotopic_interferences"
      ]
    },
    {
      "page": "cv",
      "title": "Percent coefficient of variation (%CV)",
      "topics": [
        "cv"
      ]
    },
    {
      "page": "cv_log",
      "title": "Percent coefficient of variation (%CV) based on log-transformation",
      "topics": [
        "cv_log"
      ]
    },
    {
      "page": "data_load_example",
      "title": "Load an example 'MRMhubExperiment' dataset",
      "topics": [
        "data_load_example"
      ]
    },
    {
      "page": "data_sum_features",
      "title": "Sum up feature intensities per analyte",
      "topics": [
        "data_sum_features"
      ]
    },
    {
      "page": "detect_outlier_pca",
      "title": "Get list of analyses classified as technical outliers",
      "topics": [
        "detect_outlier_pca"
      ]
    },
    {
      "page": "exclude_analyses",
      "title": "Exclude analyses from the dataset",
      "topics": [
        "exclude_analyses"
      ]
    },
    {
      "page": "exclude_features",
      "title": "Exclude features from the dataset",
      "topics": [
        "exclude_features"
      ]
    },
    {
      "page": "filter_features_qc",
      "title": "Feature filtering based on QC criteria",
      "topics": [
        "filter_features_qc"
      ]
    },
    {
      "page": "fun_cspline",
      "title": "Cubic spline smoothing helper function",
      "topics": [
        "fun_cspline"
      ]
    },
    {
      "page": "fun_gam_smooth",
      "title": "Generalized additive model (GAM) smoothing helper function",
      "topics": [
        "fun_gam_smooth"
      ]
    },
    {
      "page": "fun_gauss.kernel.smooth",
      "title": "Gaussian kernel smoothing helper function",
      "topics": [
        "fun_gauss.kernel.smooth"
      ]
    },
    {
      "page": "fun_loess",
      "title": "Loess smoothing helper function",
      "topics": [
        "fun_loess"
      ]
    },
    {
      "page": "generate_workflow_qmd",
      "title": "Generate a runnable Quarto (.qmd) mrmhub workflow",
      "topics": [
        "generate_workflow_qmd"
      ]
    },
    {
      "page": "get_analyis_end",
      "title": "Get the end time of the analysis sequence",
      "topics": [
        "get_analyis_end"
      ]
    },
    {
      "page": "get_analyis_start",
      "title": "Get the start time of the analysis sequence",
      "topics": [
        "get_analyis_start"
      ]
    },
    {
      "page": "get_analysis_breaks",
      "title": "Get the number of analysis breaks in the analysis",
      "topics": [
        "get_analysis_breaks"
      ]
    },
    {
      "page": "get_analysis_count",
      "title": "Get the number of analyses in the dataset",
      "topics": [
        "get_analysis_count"
      ]
    },
    {
      "page": "get_analysis_duration",
      "title": "Get the total duration of the analysis",
      "topics": [
        "get_analysis_duration"
      ]
    },
    {
      "page": "get_analyticaldata",
      "title": "Get the annotated or the originally imported analytical data",
      "topics": [
        "get_analyticaldata"
      ]
    },
    {
      "page": "get_batch_boundaries",
      "title": "Get the start and end analysis numbers of specified batches",
      "topics": [
        "get_batch_boundaries"
      ]
    },
    {
      "page": "get_calibration_metrics",
      "title": "Get calibration metrics",
      "topics": [
        "get_calibration_metrics"
      ]
    },
    {
      "page": "get_feature_count",
      "title": "Get the number of features in the dataset",
      "topics": [
        "get_feature_count"
      ]
    },
    {
      "page": "get_featurelist",
      "title": "Get feature IDs",
      "topics": [
        "get_featurelist"
      ]
    },
    {
      "page": "get_iqr_tails",
      "title": "Get Tukey's IQR fences",
      "topics": [
        "get_iqr_tails"
      ]
    },
    {
      "page": "get_mad_tails",
      "title": "Get MAD-based tails",
      "topics": [
        "get_mad_tails"
      ]
    },
    {
      "page": "get_outlier_bounds",
      "title": "Get outlier bounds via different methods",
      "topics": [
        "get_outlier_bounds"
      ]
    },
    {
      "page": "get_qc_bias_variability",
      "title": "Retrieve QC bias and variability metrics",
      "topics": [
        "get_qc_bias_variability"
      ]
    },
    {
      "page": "get_response_curve_stats",
      "title": "Linear regression statistics of response curves",
      "topics": [
        "get_response_curve_stats"
      ]
    },
    {
      "page": "get_runtime_median",
      "title": "Get the median run time",
      "topics": [
        "get_runtime_median"
      ]
    },
    {
      "page": "import_data_csv_long",
      "title": "Import analysis results from long-format CSV files",
      "topics": [
        "import_data_csv_long"
      ]
    },
    {
      "page": "import_data_csv_wide",
      "title": "Import analysis results from plain wide-format CSV files",
      "topics": [
        "import_data_csv_wide"
      ]
    },
    {
      "page": "import_data_masshunter",
      "title": "Import Agilent MassHunter Quantitative Analysis CSV files",
      "topics": [
        "import_data_masshunter"
      ]
    },
    {
      "page": "import_data_mrmhub",
      "title": "Import MRMhub peak integration results",
      "topics": [
        "import_data_mrmhub"
      ]
    },
    {
      "page": "import_data_mztab",
      "title": "Import data from an mzTab-M file",
      "topics": [
        "import_data_mztab"
      ]
    },
    {
      "page": "import_data_skyline",
      "title": "Import Skyline peak integration results",
      "topics": [
        "import_data_skyline"
      ]
    },
    {
      "page": "import_metadata_analyses",
      "title": "Import analysis metadata",
      "topics": [
        "import_metadata_analyses"
      ]
    },
    {
      "page": "import_metadata_features",
      "title": "Import feature metadata",
      "topics": [
        "import_metadata_features"
      ]
    },
    {
      "page": "import_metadata_from_data",
      "title": "Retrieve metadata from imported analysis data",
      "topics": [
        "import_metadata_from_data"
      ]
    },
    {
      "page": "import_metadata_istds",
      "title": "Import internal standards (ISTD) metadata",
      "topics": [
        "import_metadata_istds"
      ]
    },
    {
      "page": "import_metadata_msorganiser",
      "title": "Import metadata from a MRMhub Metadata Organizer file",
      "topics": [
        "import_metadata_msorganiser"
      ]
    },
    {
      "page": "import_metadata_qcconcentrations",
      "title": "Import calibration curves metadata",
      "topics": [
        "import_metadata_qcconcentrations"
      ]
    },
    {
      "page": "import_metadata_responsecurves",
      "title": "Import response curves metadata",
      "topics": [
        "import_metadata_responsecurves"
      ]
    },
    {
      "page": "licar_pattern_choices",
      "title": "Valid MRM-pattern labels",
      "topics": [
        "licar_pattern_choices"
      ]
    },
    {
      "page": "lipidomics_dataset",
      "title": "Plasma lipidomics dataset with metadata",
      "topics": [
        "lipidomics_dataset"
      ]
    },
    {
      "page": "mrmhub_enable_cli_color",
      "title": "Enable coloured mrmhub console output in notebooks",
      "topics": [
        "mrmhub_enable_cli_color"
      ]
    },
    {
      "page": "mrmhub_get_plot_defaults",
      "title": "Report the global MRMhub plot defaults",
      "topics": [
        "mrmhub_get_plot_defaults"
      ]
    },
    {
      "page": "mrmhub_reset_plot_defaults",
      "title": "Clear the global MRMhub plot defaults",
      "topics": [
        "mrmhub_reset_plot_defaults"
      ]
    },
    {
      "page": "mrmhub_set_plot_defaults",
      "title": "Set global default appearance for MRMhub plots",
      "topics": [
        "mrmhub_set_plot_defaults"
      ]
    },
    {
      "page": "mrmhub_status",
      "title": "Detailed processing and metadata report for a 'MRMhubExperiment'",
      "topics": [
        "mrmhub_status"
      ]
    },
    {
      "page": "MRMhubExperiment",
      "title": "Constructor for the 'MRMhubExperiment' object",
      "topics": [
        "MRMhubExperiment"
      ]
    },
    {
      "page": "MRMhubExperiment-class",
      "title": "S4 class representing the MRMhub dataset",
      "topics": [
        "MRMhubExperiment-class"
      ]
    },
    {
      "page": "normalize_by_istd",
      "title": "Normalize feature intensities using internal standards",
      "topics": [
        "normalize_by_istd"
      ]
    },
    {
      "page": "parse_lipid_feature_names",
      "title": "Get lipid class, species and transition names",
      "topics": [
        "parse_lipid_feature_names"
      ]
    },
    {
      "page": "parse_masshunter_csv",
      "title": "Reads and parses one Agilent MassHunter Quant CSV result file",
      "topics": [
        "parse_masshunter_csv"
      ]
    },
    {
      "page": "parse_mrmhub_result",
      "title": "Parses MRMhub peak integration results into a tibble",
      "topics": [
        "parse_mrmhub_result"
      ]
    },
    {
      "page": "parse_plain_long_csv",
      "title": "Parses a plain long CSV file",
      "topics": [
        "parse_plain_long_csv"
      ]
    },
    {
      "page": "parse_plain_wide_csv",
      "title": "Parses a plain wide CSV file",
      "topics": [
        "parse_plain_wide_csv"
      ]
    },
    {
      "page": "parse_skyline_result",
      "title": "Parses skyline peak integration results into a tibble",
      "topics": [
        "parse_skyline_result"
      ]
    },
    {
      "page": "plot_abundanceprofile",
      "title": "Plot abundance profile",
      "concept": [
        "EDA plots"
      ],
      "topics": [
        "plot_abundanceprofile"
      ]
    },
    {
      "page": "plot_calibrationcurves",
      "title": "Plot calibration curves",
      "concept": [
        "calibration plots"
      ],
      "topics": [
        "plot_calibrationcurves"
      ]
    },
    {
      "page": "plot_feature_correlations",
      "title": "Plot highly correlated feature pairs",
      "concept": [
        "QC plots"
      ],
      "topics": [
        "plot_feature_correlations"
      ]
    },
    {
      "page": "plot_interference_correction",
      "title": "Plot the results of interference correction",
      "concept": [
        "QC plots"
      ],
      "topics": [
        "plot_interference_correction"
      ]
    },
    {
      "page": "plot_matrixeffects",
      "title": "Plot standardized feature intensities grouped by QC type",
      "concept": [
        "QC plots"
      ],
      "topics": [
        "plot_matrixeffects"
      ]
    },
    {
      "page": "plot_normalization_qc",
      "title": "Compare feature variability before and after normalization",
      "concept": [
        "QC plots"
      ],
      "topics": [
        "plot_normalization_qc"
      ]
    },
    {
      "page": "plot_pca",
      "title": "PCA plot for quality control",
      "concept": [
        "QC plots"
      ],
      "topics": [
        "plot_pca"
      ]
    },
    {
      "page": "plot_pca_loading",
      "title": "Plot PCA loadings",
      "concept": [
        "QC plots"
      ],
      "topics": [
        "plot_pca_loading"
      ]
    },
    {
      "page": "plot_qc_interference_impact",
      "title": "Plot the magnitude of interference correction as a histogram",
      "concept": [
        "QC plots"
      ],
      "topics": [
        "plot_qc_interference_impact"
      ]
    },
    {
      "page": "plot_qc_summary_byclass",
      "title": "Plot QC filtering summary by feature class",
      "concept": [
        "QC plots"
      ],
      "topics": [
        "plot_qc_summary_byclass"
      ]
    },
    {
      "page": "plot_qc_summary_overall",
      "title": "Plot overall QC filtering summary",
      "concept": [
        "QC plots"
      ],
      "topics": [
        "plot_qc_summary_overall"
      ]
    },
    {
      "page": "plot_qcmetrics_comparison",
      "title": "Comparison of two feature QC metrics variables",
      "concept": [
        "QC plots"
      ],
      "topics": [
        "plot_qcmetrics_comparison"
      ]
    },
    {
      "page": "plot_responsecurves",
      "title": "Plot response curves",
      "concept": [
        "calibration plots"
      ],
      "topics": [
        "plot_responsecurves"
      ]
    },
    {
      "page": "plot_rla_boxplot",
      "title": "Relative log abundance (RLA) plot",
      "concept": [
        "QC plots"
      ],
      "topics": [
        "plot_rla_boxplot"
      ]
    },
    {
      "page": "plot_rt_vs_chain",
      "title": "Plot retention time versus chain length and saturation",
      "concept": [
        "QC plots"
      ],
      "topics": [
        "plot_rt_vs_chain"
      ]
    },
    {
      "page": "plot_runscatter",
      "title": "RunScatter plot",
      "concept": [
        "QC plots"
      ],
      "topics": [
        "plot_runscatter"
      ]
    },
    {
      "page": "plot_runsequence",
      "title": "RunSequence plot",
      "concept": [
        "QC plots"
      ],
      "topics": [
        "plot_runsequence"
      ]
    },
    {
      "page": "pooled_rsd",
      "title": "Pooled percent relative standard deviation (%RSD) across groups",
      "topics": [
        "pooled_rsd"
      ]
    },
    {
      "page": "pooled_sd",
      "title": "Pooled standard deviation across groups",
      "topics": [
        "pooled_sd"
      ]
    },
    {
      "page": "quant_lcms_dataset",
      "title": "LC-MS dataset with external calibration curve and metadata",
      "topics": [
        "quant_lcms_dataset"
      ]
    },
    {
      "page": "quantify_by_calibration",
      "title": "Calculate concentrations based on external calibration",
      "topics": [
        "quantify_by_calibration"
      ]
    },
    {
      "page": "quantify_by_istd",
      "title": "Calculate analyte concentrations using internal standards",
      "topics": [
        "quantify_by_istd"
      ]
    },
    {
      "page": "read_dataset_rds",
      "title": "Read a complete 'MRMhubExperiment' from an RDS file",
      "topics": [
        "read_dataset_rds"
      ]
    },
    {
      "page": "save_dataset_csv",
      "title": "Export data to a CSV file",
      "topics": [
        "save_dataset_csv"
      ]
    },
    {
      "page": "save_dataset_mztab",
      "title": "Export an experiment to mzTab-M (HUPO-PSI)",
      "topics": [
        "save_dataset_mztab"
      ]
    },
    {
      "page": "save_dataset_rds",
      "title": "Save a complete 'MRMhubExperiment' as an RDS file",
      "topics": [
        "save_dataset_rds"
      ]
    },
    {
      "page": "save_dataset_summarizedexperiment",
      "title": "Export an experiment to a Bioconductor SummarizedExperiment",
      "topics": [
        "save_dataset_summarizedexperiment"
      ]
    },
    {
      "page": "save_feature_qc_metrics",
      "title": "Save feature QC metrics to CSV",
      "topics": [
        "save_feature_qc_metrics"
      ]
    },
    {
      "page": "save_metadata_msorganiser_template",
      "title": "Saves a MRMhub Metadata Organizer template",
      "topics": [
        "save_metadata_msorganiser_template"
      ]
    },
    {
      "page": "save_metadata_templates",
      "title": "Saves an Excel (xlsx) file with metadata templates",
      "topics": [
        "save_metadata_templates"
      ]
    },
    {
      "page": "save_plot",
      "title": "Save a plot to a file",
      "topics": [
        "save_plot"
      ]
    },
    {
      "page": "save_report_xlsx",
      "title": "Write a data-processing report (Excel)",
      "topics": [
        "save_report_xlsx"
      ]
    },
    {
      "page": "set_analysis_order",
      "title": "Set analysis order",
      "topics": [
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    },
    {
      "page": "set_intensity_var",
      "title": "Set default variable to be used as feature raw signal value",
      "topics": [
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    },
    {
      "page": "set_lipid_class",
      "title": "Set feature classes from lipid names",
      "topics": [
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      ]
    },
    {
      "page": "summarize_interferences",
      "title": "Summarize interference relationships",
      "topics": [
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    }
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  "_pkglogo": "https://github.com/SLINGhub/MRMhub/raw/HEAD/man/figures/logo.png",
  "_readme": "https://github.com/SLINGhub/MRMhub/raw/HEAD/README.md",
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      "source": "mrmhub.rmd",
      "filename": "mrmhub.html",
      "title": "MRMhub",
      "author": "Bo Burla",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Overview",
        "Usage",
        "INTEGRATOR (Peak Integration)",
        "QUANT (Postprocessing and Quality Control)",
        "Documentation",
        "Contributing",
        "Contributor Code of Conduct",
        "Dual Licensing Options",
        "For commercial use and licensing of this / these code and models, please contact -",
        "Next Steps"
      ],
      "created": "2026-06-23 03:25:58",
      "modified": "2026-10-04 18:10:46",
      "commits": 6
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