Package: AlpsNMR 4.7.1

AlpsNMR: Automated spectraL Processing System for NMR

Reads Bruker NMR data directories both zipped and unzipped. It provides automated and efficient signal processing for untargeted NMR metabolomics. It is able to interpolate the samples, detect outliers, exclude regions, normalize, detect peaks, align the spectra, integrate peaks, manage metadata and visualize the spectra. After spectra proccessing, it can apply multivariate analysis on extracted data. Efficient plotting with 1-D data is also available. Basic reading of 1D ACD/Labs exported JDX samples is also available.

Authors:Ivan Montoliu Roura [aut], Sergio Oller Moreno [aut, cre], Francisco Madrid Gambin [aut], Luis Fernandez [aut], Laura López Sánchez [ctb], Héctor Gracia Cabrera [aut], Santiago Marco Colás [aut], Nestlé Institute of Health Sciences [cph], Institute for Bioengineering of Catalonia [cph], Miller Jack [ctb]

AlpsNMR_4.7.1.tar.gz
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AlpsNMR_4.7.1.tgz(r-4.4-any)AlpsNMR_4.7.1.tgz(r-4.3-any)
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AlpsNMR.pdf |AlpsNMR.html✨
AlpsNMR/json (API)
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Bug tracker:https://github.com/sipss/alpsnmr/issues

On BioConductor:AlpsNMR-4.7.1(bioc 3.20)AlpsNMR-4.6.0(bioc 3.19)

bioconductor-package

111 exports 13 stars 2.27 score 119 dependencies

Last updated 18 days agofrom:9a68fc7858

Exports:.DollarNames%>%bp_kfold_VIP_analysisbp_VIP_analysisdownload_MTBLS242file_listerfiles_to_rDolphinfilterget_integration_with_metadatais.nmr_datasetis.nmr_dataset_1Dis.nmr_dataset_peak_tablemodels_stability_plot_bootstrapmodels_stability_plot_plsdanew_nmr_data_analysis_methodnew_nmr_datasetnew_nmr_dataset_1Dnew_nmr_dataset_peak_tablenmr_alignnmr_align_find_refnmr_autophasenmr_baseline_estimationnmr_baseline_removalnmr_baseline_thresholdnmr_baseline_threshold_plotnmr_batman_export_datasetnmr_batman_metabolites_listnmr_batman_multi_data_usernmr_batman_multi_data_user_hmdbnmr_batman_optionsnmr_batman_write_optionsnmr_build_peak_tablenmr_datanmr_data_1r_to_SummarizedExperimentnmr_data_analysisnmr_data<-nmr_dataset_loadnmr_dataset_peak_table_to_SummarizedExperimentnmr_dataset_savenmr_detect_peaksnmr_detect_peaks_plotnmr_detect_peaks_plot_overviewnmr_detect_peaks_plot_peaksnmr_detect_peaks_tune_snrnmr_exclude_regionnmr_export_data_1rnmr_get_peak_distancesnmr_identify_regions_bloodnmr_identify_regions_cellnmr_identify_regions_urinenmr_integrate_peak_positionsnmr_integrate_regionsnmr_interpolate_1Dnmr_meta_addnmr_meta_add_tidy_excelnmr_meta_exportnmr_meta_getnmr_meta_get_columnnmr_meta_groupsnmr_normalizenmr_normalize_extra_infonmr_pca_build_modelnmr_pca_loadingplotnmr_pca_outliersnmr_pca_outliers_filternmr_pca_outliers_plotnmr_pca_outliers_robustnmr_pca_plot_variancenmr_pca_scoreplotnmr_peak_clusteringnmr_peak_clustering_plotnmr_ppm_resolutionnmr_read_bruker_fidnmr_read_samplesnmr_read_samples_dirnmr_zip_bruker_samplespeaklist_accept_peakspeaklist_fit_lorentzianspermutation_test_modelpermutation_test_plotpipe_add_metadatapipe_exclude_regionspipe_filter_samplespipe_interpolate_1Dpipe_load_samplespipe_normalizationpipe_outlier_detectionpipe_peak_integrationpipe_peakdet_alignplot_bootstrap_multimodelplot_interactiveplot_plsda_multimodelplot_plsda_samplesplot_vip_scoresplot_webglplsda_auroc_vip_compareplsda_auroc_vip_methodppm_resolutionrandom_subsamplingrenamesave_files_to_rDolphinsave_profiling_outputSummarizedExperiment_to_nmr_data_1rSummarizedExperiment_to_nmr_dataset_peak_tabletidyto_ASICSto_ChemoSpecvalidate_nmr_datasetvalidate_nmr_dataset_1Dvalidate_nmr_dataset_familyvalidate_nmr_dataset_peak_table

Dependencies:askpassbase64encbaselineBHBiocParallelbslibcachemcellrangercliclustercodetoolscolorspacecorpcorcpp11crayoncurldata.tabledigestdoRNGdoSNOWdplyrellipseevaluatefansifarverfastmapfontawesomeforeachformatRfsfutile.loggerfutile.optionsgenericsggplot2ggrepelgluegridExtragtablehighrhmshtmltoolshttrigraphimputeisobanditeratorsitertoolsjquerylibjsonliteknitrlabelinglambda.rlatticelifecyclelimSolvelpSolvemagrittrMASSMassSpecWaveletMatrixmatrixStatsmemoisemgcvmimemissForestmixOmicsmunsellmvtnormnlmeopensslpcaPPpillarpkgconfigplyrprettyunitsprogresspurrrquadprogR6randomForestrappdirsrARPACKRColorBrewerRcppRcppArmadilloRcppEigenRcppGSLRcppParallelRcppZigguratreadxlrematchreshape2RfastrlangrmarkdownrngtoolsRSpectrarvestsassscalesselectrsignalsnowSparseMspeaqstringistringrsystibbletidyrtidyselecttinytexutf8vctrsviridisLitewithrxfunxml2yaml