Data processing & analysis tools for Metabolomics and other omics

ANOVA | Analysis of Variance |

as_data_frame | Convert to data.frame |

AUC | Area under ROC curve |

autoscale | Autoscaling |

balanced_accuracy | Balanced Accuracy |

blank_filter | Blank filter |

blank_filter_hist | Histogram of blank filter fold changes |

bootstrap | Bootstrap resampling |

calculate | Calculate metric |

chart_plot | 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 |

DatasetExperiment_boxplot | Feature distribution histogram |

DatasetExperiment_dist | Feature distribution histogram |

DatasetExperiment_factor_boxplot | Factor boxplot |

DatasetExperiment_heatmap | DatasetExperiment heatmap |

DFA | Discriminant Factor Analysis |

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 | Hierarchical Cluster Analysis |

hca_dendrogram | HCA dendrogram |

HSD | Tukey's Honest Significant Difference |

HSDEM | Tukey's Honest Significant Difference using estimated... |

kfoldxcv_grid | k-fold cross validation plot |

kfoldxcv_metric | kfoldxcv metric plot |

kfold_xval | k-fold cross-validation |

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 | Apply method |

model_predict | Model prediction |

model_reverse | Reverse preprocessing |

model_train | Train a model |

MTBLS79_DatasetExperiment | MTBLS79: Direct infusion mass spectrometry metabolomics... |

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 |

OPLSDA | Orthogonal Partial Least Squares regression |

OPLSR | Orthogonal Partial Least Squares regression |

pairs_filter | Pairs filter |

pareto_scale | Pareto scaling |

PCA | Principal Component Analysis (PCA) |

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 |

PLSDA | Partial least squares discriminant analysis |

plsda_feature_importance_plot | PLSDA feature importance summary plot |

plsda_predicted_plot | PLSDA predicted plot |

plsda_roc_plot | PLSDA ROC plot |

PLSR | Partial least squares regression |

plsr_cook_dist | Cook's distance barchart |

pls_regcoeff_plot | pls_regcoeff_plot class |

plsr_prediction_plot | PLSR prediction plot |

plsr_qq_plot | PLSR QQ plot |

plsr_residual_hist | PLSR residuals histogram |

pls_scores_plot | PLSDA scores plot |

pls_vip_plot | PLSDA VIP plot |

pqn_norm | Probabilistic Quotient Normalisation (PQN) |

pqn_norm_hist | PQN coefficient histogram |

prop_na | Fisher's exact test for missing values |

resample | Data resampling |

resample_chart | resample_chart class |

rsd_filter | RSD filter |

rsd_filter_hist | RSD histogram |

r_squared | Coefficient of determination (R-squared) |

run | 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-package | structToolbox: Examples of tools built using the Statistics... |

SVM | Support Vector Machine Classifier |

svm_plot_2d | SVM scatter plot |

tic_chart | Total Ion Count chart. |

tSNE | tSNE |

tSNE_scatter | Feature boxplot |

ttest | t-test |

vec_norm | Vector normalisation |

wilcox_p_hist | Histogram of p values |

wilcox_test | wilcoxon signed rank test |

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