Files in computational-metabolomics/structtoolbox

Data processing & analysis tools for Metabolomics and other omics

.github/ISSUE_TEMPLATE/issue_template.md R/AUC_metric_class.R R/DFA_class.R R/HSDEM_class.R R/HSD_class.R R/MTBLS79_dataset_class.R R/PCA_class.R R/PCA_plotfcns.R R/PLSDA_charts.R R/PLSDA_class.R R/PLSR_class.R R/anova_class.R R/as_data_frame_doc.R R/autoscale_class.R R/balanced_accuracy_class.R R/blank_filter_class.R R/bootstrap_class.R R/calculate_doc.R R/chart_plot_doc.R R/classical_lsq_class.R R/confounders_clsq_class.R R/constant_sum_norm_class.R R/corr_coef_class.R R/d_ratio_filter_class.R R/dataset_chart_classes.R R/entity_objects.R R/equal_split_class.R R/factor_barchart_class.R R/feature_plot_array_class.R R/feature_profile_class.R R/filter_by_name_class.R R/filter_na_count.R R/filter_smeta_class.R R/fisher_exact_class.R R/fold_change_class.R R/fold_change_int_class.R R/forward_selection_by_rank_class.R R/ggplot_theme_pub.R R/glog_class.R R/grid_search_1d_class.R R/hca_class.R R/kfold_xval_charts.R R/kfold_xval_class.R R/knn_impute_class.R R/kw_rank_sum_class.R R/linear_model_class.R R/log_transform.R R/mean_centre_class.R R/mean_of_medians.R R/mixed_effect_class.R R/model_apply_doc.R R/model_predict_doc.R R/model_reverse_doc.R R/model_train_doc.R R/mv_feature_filter_class.R R/mv_sample_filter_class.R R/nroot_transform_class.R R/oplsda_class.R R/oplsr_class.R R/pairs_filter_class.R R/paretoscale_class.R R/permutation_test_class.R R/permute_sample_order_class.R R/plsda_feature_significance_chart.R R/pqn_norm_method_class.R R/prop_na_class.R R/r_squared_class.R R/resample_class.R R/rsd_filter.R R/run_doc.R R/sb_corr.R R/scatter_chart_class.R R/split_data_class.R R/stratified_split_class.R R/structToolbox.R R/svm_classifier_class.R R/tSNE_class.R R/tic_chart_class.R R/ttest_class.R R/vec_norm_class.R R/wilcox_test_class.R R/zzz.R README.md man-roxygen/as_data_frame.R man-roxygen/calculate.R man-roxygen/chart_plot.R man-roxygen/common_params.R man-roxygen/model_apply.R man-roxygen/model_predict.R man-roxygen/model_reverse.R man-roxygen/model_train.R man-roxygen/run.R man/ANOVA.Rd man/AUC.Rd man/DFA.Rd man/DatasetExperiment_boxplot.Rd man/DatasetExperiment_dist.Rd man/DatasetExperiment_factor_boxplot.Rd man/DatasetExperiment_heatmap.Rd man/HCA.Rd man/HSD.Rd man/HSDEM.Rd man/MTBLS79_DatasetExperiment.Rd man/OPLSDA.Rd man/OPLSR.Rd man/PCA.Rd man/PLSDA.Rd man/PLSR.Rd man/SVM.Rd man/as_data_frame.Rd man/autoscale.Rd man/balanced_accuracy.Rd man/blank_filter.Rd man/blank_filter_hist.Rd man/bootstrap.Rd man/calculate.Rd man/chart_plot.Rd man/classical_lsq.Rd man/compare_dist.Rd man/confounders_clsq.Rd man/confounders_lsq_barchart.Rd man/confounders_lsq_boxplot.Rd man/constant_sum_norm.Rd man/corr_coef.Rd man/dfa_scores_plot.Rd man/dratio_filter.Rd man/equal_split.Rd man/feature_boxplot.Rd man/feature_profile.Rd man/feature_profile_array.Rd man/filter_by_name.Rd man/filter_na_count.Rd man/filter_smeta.Rd man/fisher_exact.Rd man/fold_change.Rd man/fold_change_int.Rd man/fold_change_plot.Rd man/forward_selection_by_rank.Rd man/fs_line.Rd man/glog_opt_plot.Rd man/glog_transform.Rd man/grid_search_1d.Rd man/gs_line.Rd man/hca_dendrogram.Rd man/kfold_xval.Rd man/kfoldxcv_grid.Rd man/kfoldxcv_metric.Rd man/knn_impute.Rd man/kw_p_hist.Rd man/kw_rank_sum.Rd man/linear_model.Rd man/log_transform.Rd man/mean_centre.Rd man/mean_of_medians.Rd man/mixed_effect.Rd man/model_apply.Rd man/model_predict.Rd man/model_reverse.Rd man/model_train.Rd man/mv_boxplot.Rd man/mv_feature_filter.Rd man/mv_feature_filter_hist.Rd man/mv_histogram.Rd man/mv_sample_filter.Rd man/mv_sample_filter_hist.Rd man/nroot_transform.Rd man/ontology_cache.Rd man/pairs_filter.Rd man/pareto_scale.Rd man/pca_biplot.Rd man/pca_correlation_plot.Rd man/pca_dstat_plot.Rd man/pca_loadings_plot.Rd man/pca_scores_plot.Rd man/pca_scree_plot.Rd man/permutation_test.Rd man/permutation_test_plot.Rd man/permute_sample_order.Rd man/pls_regcoeff_plot.Rd man/pls_scores_plot.Rd man/pls_vip_plot.Rd man/plsda_feature_importance_plot.Rd man/plsda_predicted_plot.Rd man/plsda_roc_plot.Rd man/plsr_cook_dist.Rd man/plsr_prediction_plot.Rd man/plsr_qq_plot.Rd man/plsr_residual_hist.Rd man/pqn_norm.Rd man/pqn_norm_hist.Rd man/prop_na.Rd man/r_squared.Rd man/resample.Rd man/resample_chart.Rd man/rsd_filter.Rd man/rsd_filter_hist.Rd man/run.Rd man/sb_corr.Rd man/scatter_chart.Rd man/split_data.Rd man/stratified_split.Rd man/structToolbox-package.Rd man/svm_plot_2d.Rd man/tSNE.Rd man/tSNE_scatter.Rd man/tic_chart.Rd man/ttest.Rd man/vec_norm.Rd man/wilcox_p_hist.Rd man/wilcox_test.Rd tests/testthat.R tests/testthat/test-anova.R tests/testthat/test-autoscale.R tests/testthat/test-blank-filter.R tests/testthat/test-confounders-lsq.R tests/testthat/test-constant_sum_norm.R tests/testthat/test-dataset-charts.R tests/testthat/test-dratio-filter.R tests/testthat/test-factor-barchart.R tests/testthat/test-filter-by-name.R tests/testthat/test-filter-smeta.R tests/testthat/test-fisher-exact.R tests/testthat/test-foldchange.R tests/testthat/test-glog.R tests/testthat/test-gridsearch1d.R tests/testthat/test-kfold-xval.R tests/testthat/test-knn-impute.R tests/testthat/test-log-transform.R tests/testthat/test-mixed-effects.R tests/testthat/test-mv-feature-filter.R tests/testthat/test-mv-sample-filter.R tests/testthat/test-pca.R tests/testthat/test-permutation_test.R tests/testthat/test-permute-sample-order.R tests/testthat/test-plsda.R tests/testthat/test-plsr.R tests/testthat/test-pqn-norm.R tests/testthat/test-prop-na.R tests/testthat/test-rsd-filter.R tests/testthat/test-split-data.R tests/testthat/test-ttest.R tests/testthat/test-vec-norm.R vignettes/data_analysis_omics_using_the_structtoolbox.Rmd