API for specmine
Metabolomics and Spectral Data Analysis and Mining
| Global functions | |
|---|---|
| .get_density_plot_data | Source code |
| .get_gmm_plot_data | Source code |
| .get_knn_indices | Source code |
| .get_rank_matrix | Source code |
| Hyper_method | Source code |
| Hyper_uniq_method | Source code |
| MAIT_identify_metabolites | Source code |
| Match_uniq_method | Source code |
| absorbance_to_transmittance | Source code |
| aggregate_samples | Man page |
| aov_all_vars | Man page |
| aov_one_var | Man page |
| apply_by_group | Man page |
| apply_by_groups | Man page |
| apply_filter_function | Source code |
| background_correction | Source code |
| baseline_correction | Man page Source code |
| boxplot_vars_factor | Source code |
| calculate_ellipses | Source code |
| cluster_quality_metrics | Source code |
| clustering | Source code |
| color_leaf | Source code |
| compare_clusterings | Source code |
| compare_embeddings | Source code |
| compounds_in_group | Source code |
| compounds_in_organism | Source code |
| continuity_metric | Source code |
| convert_chebi_to_kegg | Man page Source code |
| convert_chebi_to_spcmnm | Source code |
| convert_from_chemospec | Man page Source code |
| convert_hmdb_to_kegg | Man page Source code |
| convert_keggpathway_2_reactiongraph | Man page Source code |
| convert_multiple_spcmnm_to_kegg | Man page Source code |
| convert_spcmnm_to_kegg | Source code |
| correlation_test | Source code |
| correlations_dataset | Source code |
| correlations_test | Source code |
| count_missing_values | Man page Source code |
| count_missing_values_per_sample | Man page Source code |
| count_missing_values_per_variable | Man page Source code |
| create_dataset | Man page |
| create_metaboanalyst_mat | Source code |
| create_pathway_with_reactions | Man page Source code |
| cv | Source code |
| dataset_from_peaks | Man page |
| dbscan_analysis_dataset | Source code |
| dbscan_pairs_plot | Source code |
| dbscan_plot2D | Source code |
| dbscan_plot3D | Source code |
| dbscan_predict_newdata | Source code |
| dendrogram_plot | Source code |
| dendrogram_plot_col | Source code |
| descendMin | Source code |
| embedding_quality_metrics | Source code |
| feature_selection | Man page Source code |
| filter_feature_selection | Man page Source code |
| findEqualGreaterM | Source code |
| first_derivative | Source code |
| flat_pattern_filter | Man page |
| flat_pattern_filter_percentage | Source code |
| flat_pattern_filter_threshold | Source code |
| fold_change | Source code |
| fold_change_var | Source code |
| get_MetabolitePath | Man page Source code |
| get_OrganismsCodes | Man page Source code |
| get_cpd_names | Man page Source code |
| get_files_list_per_assay | Man page Source code |
| get_kegg_groups | Source code |
| get_metabPaths_org | Man page Source code |
| get_metabolights_study | Man page Source code |
| get_metabolights_study_files_assay | Man page Source code |
| get_metabolights_study_metadata_assay | Man page Source code |
| get_metabolights_study_samples_files | Man page Source code |
| get_organisms_in_group | Source code |
| get_paths_with_cpds_org | Man page Source code |
| get_peak_values | Man page |
| get_samples_names_dx | Man page |
| get_samples_names_spc | Source code |
| get_spcmnm_from_spcmns | Source code |
| get_x_label | Man page |
| get_x_values_as_text | Man page |
| getbynames | Source code |
| gmm_analysis_dataset | Source code |
| gmm_bic_plot | Source code |
| gmm_pairs_plot | Source code |
| gmm_plot2D | Source code |
| gmm_plot3D | Source code |
| gmm_uncertainty_plot2D | Source code |
| group_peaks_metaboanalyst | Source code |
| hdbscan_analysis_dataset | Source code |
| hdbscan_pairs_plot | Source code |
| hdbscan_plot2D | Source code |
| hdbscan_plot3D | Source code |
| hdbscan_predict_newdata | Source code |
| heatmap_correlations | Source code |
| hierarchical_clustering | Source code |
| ica_analysis_dataset | Source code |
| ica_kmeans_plot2D | Source code |
| ica_kmeans_plot3D | Source code |
| ica_loadingsplot | Source code |
| ica_pairs_kmeans_plot | Source code |
| ica_pairs_plot | Source code |
| ica_scoresplot2D | Source code |
| ica_scoresplot3D | Source code |
| identification_nmr_peaks | Source code |
| impute_nas_knn | Man page |
| impute_nas_linapprox | Source code |
| impute_nas_mean | Man page |
| impute_nas_median | Man page |
| impute_nas_value | Man page |
| isPositive | Source code |
| is_compound_in_entity | Source code |
| is_compound_in_group | Source code |
| is_compound_in_organism | Source code |
| is_group | Source code |
| is_organism | Source code |
| kmeans_clustering | Source code |
| kmeans_plot | Source code |
| kmeans_result_df | Source code |
| kruskalTest_dataset | Source code |
| ksTest_dataset | Source code |
| linreg_coef_table | Source code |
| linreg_pvalue_table | Source code |
| linreg_rsquared | Source code |
| localMax | Source code |
| match_Hyper | Source code |
| match_Match_uniq | Source code |
| mean_centering | Source code |
| merge_data_metadata | Man page Source code |
| metabolights_studies_list | Man page Source code |
| metadata_as_variables | Source code |
| missingvalues_imputation | Man page |
| ms_create_matrix | Source code |
| ms_fill_peaks | Source code |
| ms_rt_correction | Source code |
| multiClassSummary | Man page Source code |
| multifactor_aov_pvalues_table | Source code |
| multifactor_aov_varexp_table | Source code |
| multiplot | Source code |
| nmr_identification | Source code |
| offset_correction | Source code |
| pathway_analysis | Man page Source code |
| pca_analysis_dataset | Man page Source code |
| pca_biplot | Man page Source code |
| pca_biplot3D | Man page Source code |
| pca_importance | Source code |
| pca_kmeans_plot2D | Man page Source code |
| pca_kmeans_plot3D | Man page Source code |
| pca_pairs_kmeans_plot | Man page Source code |
| pca_pairs_plot | Man page Source code |
| pca_plot_3d | Man page Source code |
| pca_robust | Man page Source code |
| pca_scoresplot2D | Man page Source code |
| pca_scoresplot3D | Man page Source code |
| pca_scoresplot3D_rgl | Man page Source code |
| pca_screeplot | Man page Source code |
| peak_detection2d | Man page Source code |
| peaklist | Source code |
| peaks_to_dataset | Source code |
| plot_2d_spectra | Source code |
| plot_anova | Source code |
| plot_fold_change | Source code |
| plot_kruskaltest | Source code |
| plot_kstest | Source code |
| plot_peaks | Source code |
| plot_regression_coefs_pvalues | Source code |
| plot_ttests | Source code |
| plotvar_twofactor | Source code |
| predict_samples | Source code |
| read_csvs_folder | Man page |
| read_data_csv | Man page Source code |
| read_data_dx | Man page |
| read_data_spc | Source code |
| read_dataset_csv | Man page Source code |
| read_dataset_dx | Man page |
| read_dataset_spc | Source code |
| read_metadata | Man page Source code |
| read_ms_spec | Source code |
| read_ms_spectra | Man page Source code |
| read_multiple_csvs | Man page |
| read_spc_nosubhdr | Man page Source code |
| rectUnique | Source code |
| recursive_feature_elimination | Man page Source code |
| remove_data | Man page Source code |
| remove_data_variables | Man page Source code |
| remove_metadata_variables | Man page Source code |
| remove_samples | Man page Source code |
| remove_samples_by_na_metadata | Man page Source code |
| remove_samples_by_nas | Man page Source code |
| remove_variables_by_nas | Man page Source code |
| remove_x_values_by_interval | Man page Source code |
| savitzky_golay | Source code |
| scale_to_interval | Source code |
| score_freq | Source code |
| score_organism | Source code |
| score_solvent | Source code |
| set_groups_metaboanalyst | Source code |
| smoothing_interpolation | Source code |
| smoothing_spcbin | Source code |
| smoothing_spcloess | Source code |
| snr_all | Source code |
| snr_spectra | Source code |
| snv_dataset | Source code |
| specmine | Man page |
| specmine-package | Man page |
| specmine.bin | Source code |
| specmine.loess | Source code |
| spectra_options | Man page |
| split_line | Source code |
| split_string | Source code |
| subset_by_samples_and_xvalues | Man page Source code |
| subset_metadata | Man page Source code |
| subset_random_samples | Man page Source code |
| subset_samples | Man page Source code |
| subset_samples_by_metadata_values | Man page Source code |
| subset_x_values | Man page Source code |
| subset_x_values_by_interval | Man page Source code |
| summary_var_importance | Man page Source code |
| tTests_dataset | Source code |
| tTests_pvalue | Source code |
| trainClassifier | Source code |
| train_and_predict | Man page Source code |
| train_classifier | Man page Source code |
| train_models_performance | Man page Source code |
| transmittance_to_absorbance | Source code |
| trim | Source code |
| trustworthiness_metric | Source code |
| tsne_analysis_dataset | Source code |
| tsne_kmeans_plot2D | Source code |
| tsne_kmeans_plot3D | Source code |
| tsne_pairs_kmeans_plot | Source code |
| tsne_pairs_plot | Source code |
| tsne_scoresplot2D | Source code |
| tsne_scoresplot3D | Source code |
| umap_analysis_dataset | Source code |
| umap_kmeans_plot2D | Source code |
| umap_kmeans_plot3D | Source code |
| umap_pairs_kmeans_plot | Source code |
| umap_pairs_plot | Source code |
| umap_scoresplot2D | Source code |
| umap_scoresplot3D | Source code |
| uniqueness_scores | Source code |
| var_importance | Source code |
| variables_as_metadata | Source code |
| volcano_plot_fc_tt | Source code |
| wavelength.seq | Source code |
| wavelengths | Source code |
