ANOVA                   Analysis of Variance
AUC                     Area under ROC curve
DFA                     Discriminant Factor Analysis
DatasetExperiment_boxplot
                        Feature distribution histogram
DatasetExperiment_dist
                        Feature distribution histogram
DatasetExperiment_factor_boxplot
                        Factor boxplot
DatasetExperiment_heatmap
                        DatasetExperiment heatmap
HCA                     Hierarchical Cluster Analysis
HSD                     Tukey's Honest Significant Difference
HSDEM                   Tukey's Honest Significant Difference using
                        estimated marginal means
MTBLS79_DatasetExperiment
                        MTBLS79: Direct infusion mass spectrometry
                        metabolomics dataset: a benchmark for data
                        processing and quality control
PCA                     Principal Component Analysis (PCA)
PLSDA                   Partial least squares discriminant analysis
PLSR                    Partial least squares regression
SVM                     Support Vector Machine Classifier
as_data_frame           Convert to data.frame
autoscale               Autoscaling
balanced_accuracy       Balanced Accuracy
blank_filter            Blank filter
blank_filter_hist       Histogram of blank filter fold changes
bootstrap               Bootstrap resampling
calculate,AUC-method    Calculate metric
chart_plot,dfa_scores_plot,DFA-method
                        chart_plot method
classical_lsq           Univariate Classical Least Squares Regression
compare_dist            Compare distributions
confounders_clsq        Check for confounding factors
confounders_lsq_barchart
                        Confounding factor relative change barchart
confounders_lsq_boxplot
                        Confounding factor relative change boxplot
constant_sum_norm       Normalisation to constant sum
corr_coef               Correlation coefficient
dfa_scores_plot         DFA scores plot
dratio_filter           Dispersion ratio filter
equal_split             Equal group sized sampling
feature_boxplot         Feature boxplot
feature_profile         Feature profile
feature_profile_array   Feature profile
filter_by_name          Filter by name
filter_na_count         Minimum number of measured values filter
filter_smeta            Filter by sample meta data
fisher_exact            Fisher Exact Test
fold_change             Fold change
fold_change_int         Fold change for interactions between factors
fold_change_plot        Fold change plot
forward_selection_by_rank
                        Forward selection by rank
fs_line                 Forward selection line plot
glog_opt_plot           Glog optimisation
glog_transform          Generalised logarithmic transform
grid_search_1d          One dimensional grid search
gs_line                 Grid search line plot
hca_dendrogram          HCA dendrogram
kfold_xval              k-fold cross-validation
kfoldxcv_grid           k-fold cross validation plot
kfoldxcv_metric         kfoldxcv metric plot
knn_impute              kNN missing value imputation
kw_p_hist               Histogram of p values
kw_rank_sum             Kruskal-Wallis rank sum test
linear_model            Linear model
log_transform           logarithm transform
mean_centre             Mean centre
mean_of_medians         Mean of medians
mixed_effect            Mixed effects model
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              Missing value boxplots
mv_feature_filter       Filter by fraction missing values
mv_feature_filter_hist
                        Histogram of missing values per feature
mv_histogram            Missing value histogram
mv_sample_filter        Missing value sample filter
mv_sample_filter_hist   Histogram of missing values per sample
nroot_transform         nth root transform
ontology_cache          ontology cache
pairs_filter            Pairs filter
pareto_scale            Pareto scaling
pca_biplot              PCA biplot
pca_correlation_plot    PCA correlation plot
pca_dstat_plot          d-statistic plot
pca_loadings_plot       PCA loadings plot
pca_scores_plot         PCA scores plot
pca_scree_plot          Scree plot
permutation_test        Permutation test
permutation_test_plot   permutation_test_plot class
permute_sample_order    Permute Sample Order
pls_regcoeff_plot       pls_regcoeff_plot class
pls_scores_plot         PLSDA scores plot
pls_vip_plot            PLSDA VIP plot
plsda_feature_importance_plot
                        PLSDA feature importance summary plot
plsda_predicted_plot    PLSDA predicted plot
plsda_roc_plot          PLSDA ROC plot
plsr_cook_dist          Cook's distance barchart
plsr_prediction_plot    PLSR prediction plot
plsr_qq_plot            PLSR QQ plot
plsr_residual_hist      PLSR residuals histogram
pqn_norm                Probabilistic Quotient Normalisation (PQN)
pqn_norm_hist           PQN coefficient histogram
prop_na                 Fisher's exact test for missing values
r_squared               Coefficient of determination (R-squared)
resample                Data resampling
resample_chart          resample_chart class
rsd_filter              RSD filter
rsd_filter_hist         RSD histogram
run,bootstrap,DatasetExperiment,metric-method
                        Runs an iterator, applying the chosen model
                        multiple times.
sb_corr                 Signal/batch correction for mass spectrometry
                        data
scatter_chart           Group scatter chart
split_data              Split data
stratified_split        Stratified sampling
structToolbox           structToolbox: Examples of tools built using
                        the Statistics in R Using Class Templates
                        (struct) package
svm_plot_2d             SVM scatter plot
tSNE                    tSNE
tSNE_scatter            Feature boxplot
tic_chart               Total Ion Count chart.
ttest                   t-test
vec_norm                Vector normalisation
wilcox_p_hist           Histogram of p values
wilcox_test             wilcoxon signed rank test
