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
OPLSDA                  Orthogonal Partial Least Squares regression
OPLSR                   Orthogonal Partial Least Squares regression
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 features by 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
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
