Files in sipss/AlpsNMR

Automated spectraL Processing System for NMR

NEWS.md R/AlpsNMR.R R/area_estimation.R R/batman_helpers.R R/bruker.R R/computes_peak_width_ppm.R R/download_MTBLS242.R R/file_lister.R R/import_jdx.R R/nmr_autophase.R R/nmr_baseline_removal.R R/nmr_baseline_threshold.R R/nmr_data.R R/nmr_data_analysis.R R/nmr_dataset.R R/nmr_dataset_1D.R R/nmr_dataset_family.R R/nmr_dataset_load_save.R R/nmr_dataset_peak_table.R R/nmr_detect_peaks_align.R R/nmr_exclude_region.R R/nmr_identify_regions.R R/nmr_integrate_regions.R R/nmr_interpolate.R R/nmr_meta.R R/nmr_normalize.R R/nmr_peak_clustering.R R/pca_helpers.R R/pipeline.R R/plots.R R/plsda.R R/to_rDolphin_blood.R R/utils.R R/zzz.R README.md inst/pipeline-rmd/add-metadata.Rmd inst/pipeline-rmd/pipeline_example.R man/AlpsNMR-package.Rd man/HMDB_blood.Rd man/HMDB_cell.Rd man/HMDB_urine.Rd man/Parameters_blood.Rd man/Parameters_cell.Rd man/Parameters_urine.Rd man/Peak_detection.Rd man/Pipelines.Rd man/ROI_blood.Rd man/ROI_cell.Rd man/ROI_urine.Rd man/SummarizedExperiment_to_nmr_data_1r.Rd man/SummarizedExperiment_to_nmr_dataset_peak_table.Rd man/bp_VIP_analysis.Rd man/bp_kfold_VIP_analysis.Rd man/download_MTBLS242.Rd man/file_lister.Rd man/files_to_rDolphin.Rd man/filter.nmr_dataset_family.Rd man/format.nmr_dataset.Rd man/format.nmr_dataset_1D.Rd man/format.nmr_dataset_peak_table.Rd man/get_integration_with_metadata.Rd man/hmdb.Rd man/is.nmr_dataset.Rd man/is.nmr_dataset_1D.Rd man/is.nmr_dataset_peak_table.Rd man/load_and_save_functions.Rd man/models_stability_plot_bootstrap.Rd man/models_stability_plot_plsda.Rd man/new_nmr_dataset.Rd man/new_nmr_dataset_1D.Rd man/new_nmr_dataset_peak_table.Rd man/nmr_align.Rd man/nmr_align_find_ref.Rd man/nmr_autophase.Rd man/nmr_baseline_estimation.Rd man/nmr_baseline_removal.Rd man/nmr_baseline_threshold.Rd man/nmr_baseline_threshold_plot.Rd man/nmr_batman.Rd man/nmr_batman_options.Rd man/nmr_build_peak_table.Rd man/nmr_data.Rd man/nmr_data_1r_to_SummarizedExperiment.Rd man/nmr_data_analysis.Rd man/nmr_data_analysis_method.Rd man/nmr_dataset.Rd man/nmr_dataset_1D.Rd man/nmr_dataset_family.Rd man/nmr_dataset_peak_table.Rd man/nmr_dataset_peak_table_to_SummarizedExperiment.Rd man/nmr_detect_peaks.Rd man/nmr_detect_peaks_plot.Rd man/nmr_detect_peaks_plot_overview.Rd man/nmr_detect_peaks_plot_peaks.Rd man/nmr_detect_peaks_tune_snr.Rd man/nmr_exclude_region.Rd man/nmr_export_data_1r.Rd man/nmr_get_peak_distances.Rd man/nmr_identify_regions_blood.Rd man/nmr_identify_regions_cell.Rd man/nmr_identify_regions_urine.Rd man/nmr_integrate_peak_positions.Rd man/nmr_integrate_regions.Rd man/nmr_interpolate_1D.Rd man/nmr_meta_add.Rd man/nmr_meta_export.Rd man/nmr_meta_get.Rd man/nmr_meta_get_column.Rd man/nmr_meta_groups.Rd man/nmr_normalize.Rd man/nmr_pca_build_model.Rd man/nmr_pca_outliers.Rd man/nmr_pca_outliers_filter.Rd man/nmr_pca_outliers_plot.Rd man/nmr_pca_outliers_robust.Rd man/nmr_pca_plots.Rd man/nmr_peak_clustering.Rd man/nmr_peak_clustering_plot.Rd man/nmr_ppm_resolution.Rd man/nmr_read_bruker_fid.Rd man/nmr_read_samples.Rd man/nmr_zip_bruker_samples.Rd man/peaklist_accept_peaks.Rd man/peaklist_fit_lorentzians.Rd man/permutation_test_model.Rd man/permutation_test_plot.Rd man/plot.nmr_dataset_1D.Rd man/plot_bootstrap_multimodel.Rd man/plot_interactive.Rd man/plot_plsda_multimodel.Rd man/plot_plsda_samples.Rd man/plot_vip_scores.Rd man/plot_webgl.Rd man/plsda_auroc_vip_compare.Rd man/plsda_auroc_vip_method.Rd man/ppm_resolution.Rd man/print.nmr_dataset.Rd man/print.nmr_dataset_1D.Rd man/print.nmr_dataset_peak_table.Rd man/random_subsampling.Rd man/read_bruker_pdata.Rd man/reexports.Rd man/save_files_to_rDolphin.Rd man/save_profiling_output.Rd man/sub-.nmr_dataset.Rd man/sub-.nmr_dataset_1D.Rd man/sub-.nmr_dataset_peak_table.Rd man/tidy.nmr_dataset_1D.Rd man/to_ASICS.Rd man/to_ChemoSpec.Rd man/validate_nmr_dataset.Rd man/validate_nmr_dataset_family.Rd man/validate_nmr_dataset_peak_table.Rd man/zzz.Rd tests/testthat.R tests/testthat/test-NMR_identify_regions.R tests/testthat/test-autophase.R tests/testthat/test-baseline_removal.R tests/testthat/test-for_asics.R tests/testthat/test-jdx.R tests/testthat/test-new_nmr_dataset_1d.R tests/testthat/test-nmr-data-analysis.R tests/testthat/test-nmr_data.R tests/testthat/test-normalization.R tests/testthat/test-outliers.R tests/testthat/test-peak-fitting.R tests/testthat/test-peak_detection.R tests/testthat/test-pipeline.R tests/testthat/test-random_subsampling.R tests/testthat/test-read_bruker.R tests/testthat/test-region_exclusion.R tests/testthat/test-rename.R tests/testthat/test-to_ChemoSpec.R tests/testthat/test-utils.R tests/testthat/test_adding_metadata.R tests/testthat/test_interpolation.R tests/testthat/test_machine_learning.R tests/testthat/test_rDolphin.R vignettes/Vig01-introduction-to-alpsnmr.Rmd vignettes/Vig01b-introduction-to-alpsnmr-old-api.Rmd vignettes/Vig02-handling-metadata-and-annotations.Rmd