AUC_model               Deprecated function Extracts AUC value
AlpsNMR-package         AlpsNMR: Automated spectraL Processing System
                        for NMR
HMDB_blood              The Human Metabolome DataBase multiplet table:
                        blood metabolites normally found in NMR-based
                        metabolomics
HMDB_cell               The Human Metabolome DataBase multiplet table:
                        cell metabolites normally found in NMR-based
                        metabolomics
HMDB_urine              The Human Metabolome DataBase multiplet table:
                        urine metabolites normally found in NMR-based
                        metabolomics
MUVR_model_plot         Deprecated function Model plot
Parameters_blood        to rDolphin
Parameters_cell         Parameters for cell samples profiling
Parameters_urine        Parameters for urine samples profiling
Pipelines               Pipelines
ROI_blood               ROIs for blood (plasma/serum) samples
ROI_cell                ROIs for cell samples
ROI_urine               ROIs for urine samples
SummarizedExperiment_to_nmr_data_1r
                        Import SummarizedExperiment as 1D NMR data
SummarizedExperiment_to_nmr_dataset_peak_table
                        Import SummarizedExperiment as
                        mr_dataset_peak_table
[.nmr_dataset           Extract parts of an nmr_dataset
[.nmr_dataset_1D        Extract parts of an nmr_dataset_1D
[.nmr_dataset_peak_table
                        Extract parts of an nmr_dataset_peak_table
bp_VIP_analysis         Bootstrap and permutation over PLS-VIP
bp_kfold_VIP_analysis   K-fold bootstrap and permutation over PLS-VIP
computes_peak_width_ppm
                        Peak width estimation for integration
confusion_matrix        Deprecated function Confusion matrix of the
                        MUVR model
file_lister             NMR file lister
files_to_rDolphin       Files to rDoplhin
filter.nmr_dataset_family
                        Keep samples based on metadata column criteria
format.nmr_dataset      Format for nmr_dataset
format.nmr_dataset_1D   format for nmr_dataset_1D
format.nmr_dataset_peak_table
                        Format for nmr_dataset_peak_table
hmdb                    The Human Metabolome DataBase multiplet table
is.nmr_dataset          Object is of nmr_dataset class
is.nmr_dataset_1D       Object is of nmr_dataset_1D class
is.nmr_dataset_peak_table
                        Object is of nmr_dataset_peak_table class
load_and_save_functions
                        nmr_dataset_load
model_VIP               Deprecated function Model VIP values
models_stability_plot_bootstrap
                        Models stability plot
models_stability_plot_plsda
                        Models stability plot
new_nmr_dataset         Create an nmr_dataset object
new_nmr_dataset_1D      Creates a new 1D nmr_dataset object from
                        scratch
new_nmr_dataset_peak_table
                        Creates a new nmr_dataset_peak_table object
                        from scratch
nmr_align_find_ref      Find alignment reference
nmr_baseline_removal    Baseline Removal NMR
nmr_baseline_threshold
                        Threshold estimation for peak detection
nmr_batman              Batman helpers
nmr_batman_options      Batman Options helper
nmr_data                Set/Return the full spectra matrix
nmr_data_1r_to_SummarizedExperiment
                        Export 1D NMR data to SummarizedExperiment
nmr_data_analysis       Data analysis
nmr_data_analysis_method
                        Create method for NMR data analysis
nmr_dataset             nmr_dataset (S3 class)
nmr_dataset_1D          nmr_dataset_1D (S3 class)
nmr_dataset_family      nmr_dataset like objects (S3 classes)
nmr_dataset_peak_table
                        nmr_dataset_peak_table (S3 class)
nmr_dataset_peak_table_to_SummarizedExperiment
                        Export nmr_dataset_peak_table to
                        SummarizedExperiment
nmr_exclude_region      Exclude region from samples
nmr_export_data_1r      Export 1D NMR data to a CSV file
nmr_identify_regions_blood
                        NMR peak identification (plasma/serum samples)
nmr_identify_regions_cell
                        NMR peak identification (cell samples)
nmr_identify_regions_urine
                        NMR peak identification (urine samples)
nmr_integrate_regions   Integrate regions
nmr_interpolate_1D      Interpolate a set of 1D NMR Spectra
nmr_meta_add            Add metadata to an nmr_dataset object
nmr_meta_export         Export Metadata to an Excel file
nmr_meta_get            Get metadata
nmr_meta_get_column     Get a single metadata column
nmr_normalize           Normalize nmr_dataset_1D samples
nmr_pca_build_model     Build a PCA on for an nmr_dataset
nmr_pca_outliers        Compute PCA residuals and score distance for
                        each sample
nmr_pca_outliers_filter
                        Exclude outliers
nmr_pca_outliers_plot   Plot for outlier detection diagnostic
nmr_pca_outliers_robust
                        Outlier detection through robust PCA
nmr_pca_plots           Plotting functions for PCA
nmr_ppm_resolution      PPM resolution of the spectra
nmr_read_bruker_fid     Read Free Induction Decay file
nmr_read_samples        Read NMR samples
nmr_zip_bruker_samples
                        Create one zip file for each brucker sample
                        path
p_value_perm            Deprecated function p-Value from permutation
                        test
permutation_test_model
                        Permutation test
permutation_test_plot   Permutation test plot
plot.nmr_dataset_1D     Plot an nmr_dataset_1D
plot_bootstrap_multimodel
                        Bootstrap plot predictions
plot_interactive        Plots in WebGL
plot_plsda_multimodel   Multi PLDSA model plot predictions
plot_plsda_samples      Plot PLSDA predictions
plot_vip_scores         Plot vip scores of bootstrap
plot_webgl              Plot a dataset into a HTML file
plsda_auroc_vip_compare
                        Compare PLSDA auroc VIP results
plsda_auroc_vip_method
                        Method for nmr_data_analysis (PLSDA model with
                        AUROC and VIP outputs)
ppm_VIP_vector          Feature selection and validation in
                        multivariate analysis
ppm_resolution          Unlisted PPM resolution
print.nmr_dataset       Print for nmr_dataset
print.nmr_dataset_1D    print for nmr_dataset_1D
print.nmr_dataset_peak_table
                        print for nmr_dataset_peak_table
random_subsampling      Random subsampling
rdCV_PLS_RF             Deprecated function
rdCV_PLS_RF_ML          Deprecated function Feature selection and
                        validation in MULTILEVEL analysis
read_bruker_sample      Read a Bruker sample directory
regions_from_peak_table
                        Build list of regions for peak integration
save_files_to_rDolphin
                        Save files to rDoplhin
save_profiling_output   Save rDoplhin output
to_ChemoSpec            Convert to ChemoSpec Spectra class
validate_nmr_dataset    Validate nmr_dataset objects
validate_nmr_dataset_family
                        Validate nmr_dataset_family objects
validate_nmr_dataset_peak_table
                        Validate nmr_dataset_peak_table objects
