Files in specmine
Metabolomics and Spectral Data Analysis and Mining
MD5
README.md
NAMESPACE
DESCRIPTION
R/sysdata.rda
R/peaklists.R
R/PATHWAY_ANALYSIS.R
R/structure.R
R/read.spc.modifed.R
R/get_metabolights_study.R
R/preprocessing.R
R/MAIT_metabolite_identification.R
R/filter_dataset.R
R/univariate.R
R/init.R
R/reading_data.R
R/machinelearning.R
R/NMR_metabolite_identification.R
R/read_spc.R
R/clustering.R
R/regression.R
R/read_dx.R
R/normalization.R
R/convert_chemospec.R
R/missing_values.R
R/stats.R
R/graphics.R
R/ms_functions.R
R/nmr_id_utils.R
R/peak_alignment.R
R/filters_flat.R
R/data_integration.R
R/read_NMR_spectra.R
R/pca.R
R/utils.R
R/feature_selection.R
inst/read_varian_spec_raw.py
inst/read_varian_2dspec_raw.py
inst/doc/dataset_2d_analysis.html
inst/doc/dataset_2d_analysis.R
inst/doc/dataset_2d_analysis.Rmd
build/vignette.rds
vignettes/dataset_2d_analysis.Rmd
data/spectra_options.rda
man/x_values_to_indexes.Rd
man/predict_samples.Rd
man/get_samples_names_spc.Rd
man/remove_x_values_by_interval.Rd
man/snv_dataset.Rd
man/get_MetabolitePath.Rd
man/remove_samples_by_nas.Rd
man/count_missing_values.Rd
man/plot_spectra_simple.Rd
man/read_dataset_dx.Rd
man/multiplot.Rd
man/pca_analysis_dataset.Rd
man/impute_nas_knn.Rd
man/volcano_plot_fc_tt.Rd
man/normalize.Rd
man/impute_nas_value.Rd
man/count_missing_values_per_variable.Rd
man/get_x_values_as_text.Rd
man/get_sample_2d_data.Rd
man/metabolights_studies_list.Rd
man/correlation_test.Rd
man/recursive_feature_elimination.Rd
man/subset_samples_by_metadata_values.Rd
man/impute_nas_mean.Rd
man/pca_plot_3d.Rd
man/pca_scoresplot3D_rgl.Rd
man/create_pathway_with_reactions.Rd
man/values_per_sample.Rd
man/stats_by_sample.Rd
man/merge_data_metadata.Rd
man/get_metadata.Rd
man/pca_kmeans_plot2D.Rd
man/convert_chebi_to_kegg.Rd
man/count_missing_values_per_sample.Rd
man/subset_random_samples.Rd
man/convert_to_factor.Rd
man/values_per_peak.Rd
man/pca_biplot.Rd
man/read_data_csv.Rd
man/read_multiple_csvs.Rd
man/remove_peaks_interval.Rd
man/summary_var_importance.Rd
man/msc_correction.Rd
man/remove_data.Rd
man/xvalue_interval_to_indexes.Rd
man/plot_regression_coefs_pvalues.Rd
man/subset_x_values.Rd
man/peaks_per_sample.Rd
man/replace_metadata_value.Rd
man/is_spectra.Rd
man/data_correction.Rd
man/remove_metadata_variables.Rd
man/sum_dataset.Rd
man/nmr_identification.Rd
man/read_data_dx.Rd
man/flat_pattern_filter.Rd
man/plot_spectra.Rd
man/aov_all_vars.Rd
man/fold_change_var.Rd
man/normalize_samples.Rd
man/get_sample_names.Rd
man/kmeans_clustering.Rd
man/absorbance_to_transmittance.Rd
man/impute_nas_median.Rd
man/plot_ttests.Rd
man/first_derivative.Rd
man/subset_metadata.Rd
man/detect_nmr_peaks_from_dataset.Rd
man/remove_peaks_interval_sample_list.Rd
man/get_metadata_var.Rd
man/plot_2d_spectra.Rd
man/cubic_root_transform.Rd
man/get_data.Rd
man/scaling.Rd
man/read_csvs_folder.Rd
man/train_classifier.Rd
man/get_metabPaths_org.Rd
man/convert_hmdb_to_kegg.Rd
man/read-spc.Rd
man/read_ms_spectra.Rd
man/peak_detection2d.Rd
man/dataset_from_peaks.Rd
man/linreg_rsquared.Rd
man/boxplot_vars_factor.Rd
man/get_data_value.Rd
man/hierarchical_clustering.Rd
man/set_value_label.Rd
man/set_metadata.Rd
man/low_level_fusion.Rd
man/read_metadata.Rd
man/pca_scoresplot2D.Rd
man/plot_kstest.Rd
man/read_dataset_csv.Rd
man/plot_peaks.Rd
man/log_transform.Rd
man/check_2d_dataset.Rd
man/apply_by_variable.Rd
man/set_sample_names.Rd
man/create_dataset.Rd
man/linreg_pvalue_table.Rd
man/read_varian_spectra_raw.Rd
man/get_samples_names_dx.Rd
man/transmittance_to_absorbance.Rd
man/apply_by_groups.Rd
man/subset_by_samples_and_xvalues.Rd
man/apply_by_group.Rd
man/read_Bruker_files_2d.Rd
man/pca_robust.Rd
man/linregression_onevar.Rd
man/convert_keggpathway_2_reactiongraph.Rd
man/boxplot_variables.Rd
man/convert_from_chemospec.Rd
man/read_dataset_spc.Rd
man/apply_by_sample.Rd
man/correlations_dataset.Rd
man/group_peaks.Rd
man/get_OrganismsCodes.Rd
man/subset_samples.Rd
man/get_peak_values.Rd
man/get_paths_with_cpds_org.Rd
man/pca_kmeans_plot3D.Rd
man/get_x_values_as_num.Rd
man/baseline_correction.Rd
man/read_data_spc.Rd
man/get_metabolights_study_metadata_assay.Rd
man/get_metabolights_study_samples_files.Rd
man/multifactor_aov_varexp_table.Rd
man/get_data_as_df.Rd
man/get_metabolights_study_files_assay.Rd
man/plotvar_twofactor.Rd
man/pca_biplot3D.Rd
man/pca_scoresplot3D.Rd
man/filter_feature_selection.Rd
man/MAIT_identify_metabolites.Rd
man/mean_centering.Rd
man/plot_anova.Rd
man/create_2d_dataset.Rd
man/peaks_per_samples.Rd
man/set_x_values.Rd
man/savitzky_golay.Rd
man/indexes_to_xvalue_interval.Rd
man/remove_data_variables.Rd
man/get_metabolights_study.Rd
man/multifactor_aov_all_vars.Rd
man/set_x_label.Rd
man/num_x_values.Rd
man/get_x_label.Rd
man/multifactor_aov_pvalues_table.Rd
man/linreg_all_vars.Rd
man/pca_screeplot.Rd
man/clustering.Rd
man/train_models_performance.Rd
man/kmeans_result_df.Rd
man/multiClassSummary.Rd
man/read_varian_2dspectra_raw.Rd
man/pathway_analysis.Rd
man/get_data_values.Rd
man/remove_variables_by_nas.Rd
man/kmeans_plot.Rd
man/plot_fold_change.Rd
man/train_and_predict.Rd
man/offset_correction.Rd
man/pca_importance.Rd
man/subset_x_values_by_interval.Rd
man/sum_2d_dataset.Rd
man/feature_selection.Rd
man/check_dataset.Rd
man/find_equal_samples.Rd
man/metadata_as_variables.Rd
man/remove_samples.Rd
man/fold_change.Rd
man/aggregate_samples.Rd
man/background_correction.Rd
man/get_value_label.Rd
man/correlations_test.Rd
man/transform_data.Rd
man/plot_kruskaltest.Rd
man/convert_multiple_spcmnm_to_kegg.Rd
man/smoothing_interpolation.Rd
man/scaling_samples.Rd
man/variables_as_metadata.Rd
man/pca_pairs_plot.Rd
man/dendrogram_plot.Rd
man/replace_data_value.Rd
man/get_type.Rd
man/impute_nas_linapprox.Rd
man/num_samples.Rd
man/shift_correction.Rd
man/heatmap_correlations.Rd
man/get_files_list_assay.Rd
man/dendrogram_plot_col.Rd
man/pca_pairs_kmeans_plot.Rd
man/spectra_options.Rd
man/stats_by_variable.Rd
man/kruskalTest_dataset.Rd
man/read_Bruker_files.Rd
man/missingvalues_imputation.Rd
man/remove_samples_by_na_metadata.Rd
man/get_metadata_value.Rd
man/tTests_dataset.Rd
man/linreg_coef_table.Rd
man/ksTest_dataset.Rd
man/get_cpd_names.Rd
man/merge_datasets.Rd
man/compare_regions_by_sample.Rd
