MAIT_identify_metabolites
                        MAIT metabolite identification
absorbance_to_transmittance
                        Convert absorbance to transmittance
aggregate_samples       Aggregate samples
aov_all_vars            Analysis of variance
apply_by_group          Apply by group
apply_by_groups         Apply by groups
apply_by_sample         Apply function to samples
apply_by_variable       Apply function to variables
background_correction   Background correction
baseline_correction     Baseline correction
boxplot_variables       Boxplot of variables
boxplot_vars_factor     Boxplot of variables with metadata's variable
                        factors
check_2d_dataset        Check 2D dataset.
check_dataset           Check dataset
clustering              Perform cluster analysis
compare_regions_by_sample
                        Compare regions by sample
convert_chebi_to_kegg   Convert CHEBI codes to KEGG codes.
convert_from_chemospec
                        Convert from ChemoSpec
convert_hmdb_to_kegg    Convert HMDB codes to KEGG codes.
convert_keggpathway_2_reactiongraph
                        Convert KEGGPathway object to graph object.
convert_multiple_spcmnm_to_kegg
                        Convert specmine metabolite codes to KEGG
                        codes.
convert_to_factor       Convert metadata to factor
correlation_test        Correlation test of two variables or samples
correlations_dataset    Dataset correlations
correlations_test       Correlations test
count_missing_values    Count missing values
count_missing_values_per_sample
                        Count missing values per sample
count_missing_values_per_variable
                        Count missing values per variable
create_2d_dataset       Create 2D dataset
create_dataset          Create dataset
create_pathway_with_reactions
                        Creates the pathway, with reactions included in
                        the nodes.
cubic_root_transform    Cubic root transformation
data_correction         Data correction
dataset_from_peaks      Dataset from peaks
dendrogram_plot         Plot dendrogram
dendrogram_plot_col     Plot dendrogram
detect_nmr_peaks_from_dataset
                        Detection of the peaks in an NMR spectra
                        dataset.
feature_selection       Perform feature selection
filter_feature_selection
                        Perform selection by filter
find_equal_samples      Find equal samples
first_derivative        First derivative
flat_pattern_filter     Flat pattern filter
fold_change             Fold change analysis
fold_change_var         Fold change applied on two variables
get_MetabolitePath      Returns an object of KEGGPathway of the pathway
                        especified in pathcode.
get_OrganismsCodes      Get all organisms in KEGG.
get_cpd_names           Get the names of the compounds that correspond
                        to the kegg codes given.
get_data                Get data
get_data_as_df          Get data as data frame
get_data_value          Get data value
get_data_values         Get data values
get_files_list_per_assay
                        Get list of files per assay for MetaboLights
                        study.
get_metabPaths_org      Get the metabolic pathways present in given
                        organism.
get_metabolights_study
                        Download MetaboLights study files.
get_metabolights_study_files_assay
                        Download data files from an assay of
                        MetaboLights study
get_metabolights_study_metadata_assay
                        Download metadata file from an assay of
                        MetaboLights study
get_metabolights_study_samples_files
                        Get list of files from an assay of the
                        MetaboLights study and saves it in a csv file.
get_metadata            Get metadata
get_metadata_value      Get metadata value
get_metadata_var        Get metadata variable
get_paths_with_cpds_org
                        Get only the paths of the organism that contain
                        one or more of the given compounds.
get_peak_values         Get peak values
get_sample_2d_data      Get data
get_sample_names        Get sample names
get_samples_names_dx    Get sample's names from DX files
get_samples_names_spc   Get sample's names from SPC files
get_type                Get type of data
get_value_label         Get value label
get_x_label             Get x-axis label
get_x_values_as_num     Get x-axis values as numbers
get_x_values_as_text    Get x-axis values as text
group_peaks             Group peaks
heatmap_correlations    Correlations heatmap
hierarchical_clustering
                        Perform hierarchical clustering analysis
impute_nas_knn          Impute missing values with KNN
impute_nas_linapprox    Impute missing values with linear approximation
impute_nas_mean         Impute missing values with mean
impute_nas_median       Impute missing values with median
impute_nas_value        Impute missing values with value replacement
indexes_to_xvalue_interval
                        Get the x-values of a vector of indexes
is_spectra              Check type of data
kmeans_clustering       Perform k-means clustering analysis
kmeans_plot             Plot kmeans clusters
kmeans_result_df        Show cluster's members
kruskalTest_dataset     Kruskal-Wallis tests on dataset
ksTest_dataset          Kolmogorov-Smirnov tests on dataset
linreg_all_vars         Linear Regression
linreg_coef_table       Linear regression coefficient table
linreg_pvalue_table     Linear regression p-values table
linreg_rsquared         Linear regression r-squared
linregression_onevar    Linear regression on one variable
log_transform           Logarithmic transformation.
low_level_fusion        Low level fusion
mean_centering          Mean centering
merge_data_metadata     Merge data and metadata
merge_datasets          Merge two datasets
metabolights_studies_list
                        List the study IDs available in the
                        MetaboLights database.
metadata_as_variables   Metadata as variables
missingvalues_imputation
                        Missing values imputation
msc_correction          Multiplicative scatter correction
multiClassSummary       Multi Class Summary
multifactor_aov_all_vars
                        Multifactor ANOVA
multifactor_aov_pvalues_table
                        Multifactor ANOVA p-values table
multifactor_aov_varexp_table
                        Multifactor ANOVA variability explained table
multiplot               Multiplot
nmr_identification      NMR metabolite identification
normalize               Normalize data
normalize_samples       Normalize samples
num_samples             Get number of samples
num_x_values            Get number of x values
offset_correction       Offset correction
pathway_analysis        Creates the metabolic pathway wanted. If any of
                        the given compounds is present in the pathway,
                        it is coloured differently.
pca_analysis_dataset    PCA analysis (classical)
pca_biplot              PCA biplot
pca_biplot3D            3D PCA biplot (interactive)
pca_importance          PCA importance
pca_kmeans_plot2D       2D PCA k-means plot
pca_kmeans_plot3D       3D PCA k-means plot (interactive)
pca_pairs_kmeans_plot   PCA k-means pairs plot
pca_pairs_plot          PCA pairs plot
pca_plot_3d             3D pca plot
pca_robust              PCA analysis (robust)
pca_scoresplot2D        2D PCA scores plot
pca_scoresplot3D        3D PCA scores plot
pca_scoresplot3D_rgl    3D PCA scores plot (interactive)
pca_screeplot           PCA scree plot
peak_detection2d        Detection of the peaks in an 2D NMR spectra
                        dataset.
peaks_per_sample        Peaks per sample
peaks_per_samples       Peaks per samples
plot_2d_spectra         Plot of 2D spectra
plot_anova              Plot ANOVA results
plot_fold_change        Plot fold change results
plot_kruskaltest        Plot Kruskal-Wallis tests results
plot_kstest             Plot Kolmogorov-Smirnov tests results
plot_peaks              Plot the peaks of a MS or NMR dataset.
plot_regression_coefs_pvalues
                        Plot regression coefficient and p-values
plot_spectra            Plot spectra
plot_spectra_simple     Plot spectra (simple)
plot_ttests             Plot t-tests results
plotvar_twofactor       Plot variable distribution on two factors
predict_samples         Predict samples
read_Bruker_files       Read Bruker processed spectra.
read_Bruker_files_2d    Read Bruker processed 2D spectra.
read_csvs_folder        Read CSVs from folder
read_data_csv           Read CSV data
read_data_dx            Read data from (J)DX files
read_data_spc           Read data from SPC files
read_dataset_csv        Read dataset from CSV
read_dataset_dx         Read dataset from (J)DX files
read_dataset_spc        Read dataset from SPC files
read_metadata           Read metadata
read_ms_spectra         Read MS spectra
read_multiple_csvs      Read multiple CSVs
read_spc_nosubhdr       Import for Thermo Galactic's spc file format
                        These functions allow to import .spc files.
read_varian_2dspectra_raw
                        Function that reads raw 2D spectra (intensity
                        over time spectra) from the varian format and
                        processes them to ppm spectra.
read_varian_spectra_raw
                        Function that reads raw spectra (intensity over
                        time spectra) from the varian format and
                        processes them to ppm spectra.
recursive_feature_elimination
                        Perform recursive feature elimination
remove_data             Remove data
remove_data_variables   Remove data variables
remove_metadata_variables
                        Remove metadata's variables
remove_peaks_interval   Remove interval of peaks
remove_peaks_interval_sample_list
                        Remove interval of peaks (sample list)
remove_samples          Remove samples
remove_samples_by_na_metadata
                        Remove samples by NA on metadata
remove_samples_by_nas   Remove samples by NAs
remove_variables_by_nas
                        Remove variables by NAs
remove_x_values_by_interval
                        Remove x-values by interval
replace_data_value      Replace data value
replace_metadata_value
                        Replace metadata's value
savitzky_golay          Savitzky-golay transformation
scaling                 Scale dataset
scaling_samples         Scale data matrix
set_metadata            Set new metadata
set_sample_names        Set samples names
set_value_label         Set value label
set_x_label             Set x-label
set_x_values            Set new x-values
shift_correction        Shift correction
smoothing_interpolation
                        Smoothing interpolation
snv_dataset             Standard Normal Variate
spectra_options         Information on the library of NMR reference
                        spectra in our package.
stats_by_sample         Statistics of samples
stats_by_variable       Statistics of variables
subset_by_samples_and_xvalues
                        Subset by samples and x-values
subset_metadata         Subset metadata
subset_random_samples   Subset random samples
subset_samples          Subset samples
subset_samples_by_metadata_values
                        Subset samples by metadata values
subset_x_values         Subset x-values
subset_x_values_by_interval
                        Subset x-values by interval
sum_2d_dataset          2D Dataset summary
sum_dataset             Dataset summary
summary_var_importance
                        Summary of variables importance
tTests_dataset          t-Tests on dataset
train_and_predict       Train and predict
train_classifier        Train classifier
train_models_performance
                        Train models
transform_data          Transform data
transmittance_to_absorbance
                        Convert transmittance to absorbance
values_per_peak         Values per peak
values_per_sample       Values per peak
variables_as_metadata   Variables as metadata
volcano_plot_fc_tt      Volcano plot
x_values_to_indexes     Get x-values indexes
xvalue_interval_to_indexes
                        Get indexes of an interval of x-values
