ANOVA                   ANOVA
AUC                     Area under ROC
DFA                     Discriminant Factor Analysis (DFA)
DatasetExperiment_boxplot
                        DatasetExperiment boxplot
DatasetExperiment_dist
                        Distribution plot
DatasetExperiment_factor_barchart
                        DatasetExperiment_factor_barchart class
DatasetExperiment_heatmap
                        DatasetExperiment_heatmap class
HCA                     HCA method class
HSD                     HSD model class
HSDEM                   HSD model class using estimated marginal means
MTBLS79_DatasetExperiment
                        MTBLS79: Direct infusion mass spectrometry
                        metabolomics dataset: a benchmark for data
                        processing and quality control
PCA                     PCA model class
PLSDA                   PLSDA model class
PLSR                    PLSR model class
SVM                     SVM model classifier
as_data_frame           Convert to data.frame
autoscale               Autoscale
balanced_accuracy       Balanced Accuracy
blank_filter            Blank filter
blank_filter_hist       plot for blank filter
bootstrap               Bootstrap class
calculate,AUC-method    Calculate metric
chart_plot,dfa_scores_plot,DFA-method
                        chart_plot method
classical_lsq           Classical Least Squares regression
compare_dist            Compare distributions
confounders_clsq        Check for confounding factors in ttest
confounders_lsq_barchart
                        barchart of percent change
confounders_lsq_boxplot
                        boxplot of percent change
constant_sum_norm       Normalisation to constant sum
corr_coef               Correlation Coefficient
dfa_scores_plot         dfa_scores_plot class
dratio_filter           D ratio filter
feature_boxplot         Feature boxplots
feature_profile         Feature profile class
filter_by_name          Filter by name
filter_na_count         filter_na_count class
filter_smeta            filter_smeta class
fisher_exact            fisher_exact class
fold_change             fold change class
fold_change_int         fold change for interactions class
fold_change_plot        fold_change plot
forward_selection_byrank
                        forward selection by rank
fs_line                 forward_selection_plot
glog_opt_plot           glog transform optimisation plot
glog_transform          glog transform
grid_search_1d          grid_search_1d class
gs_line                 grid_search_plot
hca_dendrogram          hca_dendrogram class
kfold_xval              kfold_xval model class
kfoldxcv_grid           kfoldxcv_grid class
kfoldxcv_metric         kfoldxcv_metric class
knn_impute              knn missing value imputation
kw_p_hist               plot histogram of p values
kw_rank_sum             kruskal-wallis model class
linear_model            linear model class
log_transform           log transform
mean_centre             mean_centre model class
mean_of_medians         Mean of median adjustment
mixed_effect            Mixed Effects model class
model_apply,ANOVA,DatasetExperiment-method
                        Apply method
model_predict,DFA,DatasetExperiment-method
                        Model prediction
model_reverse,autoscale,DatasetExperiment-method
                        Reverse preprocessing
model_train,DFA,DatasetExperiment-method
                        Train a model
mv_boxplot              mv_boxplot class
mv_feature_filter       filter features by fraction of missing values
mv_feature_filter_hist
                        plot for missing value sample filter
mv_histogram            mv_histogram class
mv_sample_filter        Missing value filter (samples)
mv_sample_filter_hist   plot for missing value sample filter
nroot_transform         nroot transform
pairs_filter            Pairs filter
pareto_scale            Pareto scaling
pca_biplot_plot         pca_biplot_plot class
pca_correlation_plot    pca_correlation_plot class
pca_dstat_plot          pca_dstat_plot_plot class
pca_loadings_plot       pca_loadings_plot class
pca_scores_plot         pca_scores_plot class
pca_scree_plot          pca_scree_plot_plot class
permutation_test        Permutation test class
permutation_test_plot   permutation_test_plot class
permute_sample_order    permute_sample_order class
plsda_predicted_plot    plsda_predicted_plot class
plsda_regcoeff_plot     plsda_regcoeff_plot class
plsda_roc_plot          plsda_roc_plot class
plsda_scores_plot       plsda_scores_plot class
plsda_vip_plot          plsda_vip_plot class
plsr_cook_dist          plsr_cook_dist class
plsr_prediction_plot    plsr_prediction_plot class
plsr_qq_plot            plsr_qq_plot class
plsr_residual_hist      plsr_residual_hist class
pqn_norm                Probabilistic Quotient Normalisation
pqn_norm_hist           plot for PQN normalisation
prop_na                 prop_na model class
r_squared               Coefficient of determination class
rsd_filter              rsd filter
rsd_filter_hist         plot for rsd filter
run,bootstrap,DatasetExperiment,metric-method
                        Runs an iterator, applying the chosen model
                        multiple times.
sb_corr                 sbcms
split_data              Split data into subsets
stratified_split        Stratified sampling
structToolbox           structToolbox: Examples of tools built using
                        the Statistics in R Using Class Templates
                        (struct) package
svm_plot_2d             SVM boundary plot (2d)
tSNE                    tSNE method class
tSNE_scatter            tSNE_scatter class
ttest                   t-test model class
vec_norm                Vector normalisation
wilcox_p_hist           plot histogram of p values
wilcox_test             Wilcoxon signed rank test method class
