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
Parameters_blood        to rDolphin
Parameters_cell         Parameters for cell samples profiling
Parameters_urine        Parameters for urine samples profiling
Peak_detection          Peak detection for NMR
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
download_MTBLS242       Download MTBLS242
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
get_integration_with_metadata
                        Get integrals with metadata from integrate peak
                        positions
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
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               Align NMR spectra
nmr_align_find_ref      Find alignment reference
nmr_autophase           Rephase 1D NMR data
nmr_baseline_estimation
                        Estimate the baseline on an nmr_dataset_1D
                        object, using baseline::baseline.als.
nmr_baseline_removal    Baseline Removal NMR
nmr_baseline_threshold
                        Threshold estimation for peak detection
nmr_baseline_threshold_plot
                        Plot the baseline thresholds
nmr_batman              Batman helpers
nmr_batman_options      Batman Options helper
nmr_build_peak_table    Build a peak table from the clustered peak list
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_detect_peaks        Peak detection for NMR
nmr_detect_peaks_plot   Plot peak detection results
nmr_detect_peaks_plot_overview
                        Overview of the peak detection results
nmr_detect_peaks_plot_peaks
                        Plot multiple peaks from a peak list
nmr_detect_peaks_tune_snr
                        Diagnose SNR threshold in peak detection
nmr_exclude_region      Exclude region from samples
nmr_export_data_1r      Export 1D NMR data to a CSV file
nmr_get_peak_distances
                        Compute peak to peak distances
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_peak_positions
                        Integrate peak positions
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_meta_groups         Get the names of metadata groups
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_peak_clustering     Peak clustering
nmr_peak_clustering_plot
                        Plot clustering results
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
peaklist_accept_peaks   Peak list: Create an 'accepted' column based on
                        some criteria
peaklist_fit_lorentzians
                        Fit lorentzians to each peak to estimate areas
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_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
save_files_to_rDolphin
                        Save files to rDoplhin
save_profiling_output   Save rDoplhin output
tidy.nmr_dataset_1D     Get a tidy data frame from nmr_data object
to_ASICS                Export data for the ASICS spectral
                        quantification library
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
