Package: structToolbox
Type: Package
Title: Data processing & analysis tools for Metabolomics and other
        omics
Version: 1.22.0
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). The STATistics Ontology (STATO) has
        been integrated and implemented 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, methods, scales, sp, stats
RoxygenNote: 7.3.1
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/pak/sysreqs: libicu-dev libssl-dev zlib1g-dev
Repository: https://bioc-release.r-universe.dev
Date/Publication: 2025-10-29 14:56:35 UTC
RemoteUrl: https://github.com/bioc/structToolbox
RemoteRef: RELEASE_3_22
RemoteSha: cad0ce8079d81192cc1a62a7c3dc682b222e4f53
NeedsCompilation: no
Packaged: 2025-12-24 08:38:09 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>
Built: R 4.5.2; ; 2025-12-24 08:40:25 UTC; windows
