Package: structToolbox
Type: Package
Title: Data processing & analysis tools for Metabolomics and other
        omics
Version: 1.24.0
Authors@R: c(
    person(
        c("Gavin","Rhys"),
          "Lloyd",
           role=c("aut","cre"),
           email="g.r.lloyd@bham.ac.uk",
		   comment = c(ORCID = "0000-0001-7989-6695")
		),
    person(
        c("Ralf","Johannes", "Maria"),
          "Weber",
           role=c("aut"),
           email="r.j.weber@bham.ac.uk")
        )
Description: An extensive set of data (pre-)processing and analysis
        methods and tools for metabolomics and other omics, with a
        strong emphasis on statistics and machine learning. This
        toolbox allows the user to build extensive and standardised
        workflows for data analysis. The methods and tools have been
        implemented using class-based templates provided by the struct
        (Statistics in R Using Class-based Templates) package. The
        toolbox includes pre-processing methods (e.g. signal drift and
        batch correction, normalisation, missing value imputation and
        scaling), univariate (e.g. ttest, various forms of ANOVA,
        Kruskal–Wallis test and more) and multivariate statistical
        methods (e.g. PCA and PLS, including cross-validation and
        permutation testing) as well as machine learning methods (e.g.
        Support Vector Machines). Ontology terms have been integrated
        to provide standardised definitions for the different methods,
        inputs and outputs.
License: GPL-3
Encoding: UTF-8
Collate: 'AUC_metric_class.R' 'entity_objects.R' 'DFA_class.R' 'zzz.R'
        'anova_class.R' 'HSD_class.R' 'mixed_effect_class.R'
        'HSDEM_class.R' 'MTBLS79_dataset_class.R' 'PCA_class.R'
        'scatter_chart_class.R' 'PCA_plotfcns.R' 'PLSR_class.R'
        'PLSDA_class.R' 'PLSDA_charts.R' 'as_data_frame_doc.R'
        'autoscale_class.R' 'balanced_accuracy_class.R'
        'blank_filter_class.R' 'bootstrap_class.R' 'calculate_doc.R'
        'chart_plot_doc.R' 'classical_lsq_class.R'
        'confounders_clsq_class.R' 'constant_sum_norm_class.R'
        'corr_coef_class.R' 'd_ratio_filter_class.R'
        'dataset_chart_classes.R' 'split_data_class.R'
        'equal_split_class.R' 'factor_barchart_class.R'
        'feature_plot_array_class.R' 'feature_profile_class.R'
        'filter_by_name_class.R' 'filter_na_count.R'
        'filter_smeta_class.R' 'fisher_exact_class.R'
        'fold_change_class.R' 'fold_change_int_class.R'
        'forward_selection_by_rank_class.R' 'ggplot_theme_pub.R'
        'glog_class.R' 'grid_search_1d_class.R' 'hca_class.R'
        'kfold_xval_class.R' 'kfold_xval_charts.R' 'knn_impute_class.R'
        'kw_rank_sum_class.R' 'linear_model_class.R' 'log_transform.R'
        'mean_centre_class.R' 'mean_of_medians.R' 'model_apply_doc.R'
        'model_predict_doc.R' 'model_reverse_doc.R' 'model_train_doc.R'
        'mv_feature_filter_class.R' 'mv_sample_filter_class.R'
        'nroot_transform_class.R' 'oplsr_class.R' 'oplsda_class.R'
        'pairs_filter_class.R' 'paretoscale_class.R'
        'permutation_test_class.R' 'permute_sample_order_class.R'
        'plsda_feature_significance_chart.R' 'pqn_norm_method_class.R'
        'prop_na_class.R' 'r_squared_class.R' 'resample_class.R'
        'rsd_filter.R' 'run_doc.R' 'sb_corr.R'
        'stratified_split_class.R' 'structToolbox.R'
        'svm_classifier_class.R' 'tSNE_class.R' 'tic_chart_class.R'
        'ttest_class.R' 'vec_norm_class.R' 'wilcox_test_class.R'
Depends: R (>= 4.0), struct (>= 1.5.1)
Imports: ggplot2, ggthemes, grid, gridExtra, httr, jsonlite, methods,
        scales, sp, stats, limma
RoxygenNote: 7.3.3
Suggests: agricolae, BiocFileCache, BiocStyle, car, covr, cowplot,
        e1071, emmeans, ggdendro, knitr, magick, nlme, openxlsx, pls,
        pmp, reshape2, ropls, rmarkdown, Rtsne, testthat, rappdirs
VignetteBuilder: knitr
biocViews: WorkflowStep, Metabolomics
URL: https://github.com/computational-metabolomics/structToolbox,
        https://computational-metabolomics.github.io/structToolbox/
Roxygen: list(markdown = TRUE)
Config/Needs/website: rmarkdown
Config/pak/sysreqs: libicu-dev libssl-dev zlib1g-dev
Repository: Bioconductor 3.23
Date/Publication: 2026-04-28 12:51:44 UTC
RemoteUrl: https://github.com/bioc/structToolbox
RemoteRef: RELEASE_3_23
RemoteSha: 635292a734854826985f5e8f84ebfb4c8892fc63
NeedsCompilation: no
Packaged: 2026-07-04 10:48:39 UTC; root
Author: Gavin Rhys Lloyd [aut, cre] (ORCID:
    <https://orcid.org/0000-0001-7989-6695>),
  Ralf Johannes Maria Weber [aut]
Maintainer: Gavin Rhys Lloyd <g.r.lloyd@bham.ac.uk>