Package: AlpsNMR 4.9.0

Sergio Oller Moreno

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_4.9.0.tar.gz
AlpsNMR_4.9.0.zip(r-4.5)AlpsNMR_4.9.0.zip(r-4.4)AlpsNMR_4.9.0.zip(r-4.3)
AlpsNMR_4.9.0.tgz(r-4.4-any)AlpsNMR_4.9.0.tgz(r-4.3-any)
AlpsNMR_4.9.0.tar.gz(r-4.5-noble)AlpsNMR_4.9.0.tar.gz(r-4.4-noble)
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AlpsNMR.pdf |AlpsNMR.html✨
AlpsNMR/json (API)
NEWS

# Install 'AlpsNMR' in R:
install.packages('AlpsNMR', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/sipss/alpsnmr/issues

Pkgdown:https://sipss.github.io

Datasets:
  • HMDB_blood - The Human Metabolome DataBase multiplet table: blood metabolites normally found in NMR-based metabolomics
  • HMDB_cell - The Human Metabolome DataBase multiplet table: cell metabolites normally found in NMR-based metabolomics
  • HMDB_urine - The Human Metabolome DataBase multiplet table: urine metabolites normally found in NMR-based metabolomics
  • Parameters_blood - To rDolphin
  • Parameters_cell - Parameters for cell samples profiling
  • Parameters_urine - Parameters for urine samples profiling
  • ROI_blood - ROIs for blood (plasma/serum) samples
  • ROI_cell - ROIs for cell samples
  • ROI_urine - ROIs for urine samples
  • hmdb - The Human Metabolome DataBase multiplet table

On BioConductor:AlpsNMR-4.9.0(bioc 3.21)AlpsNMR-4.8.0(bioc 3.20)

softwarepreprocessingvisualizationclassificationcheminformaticsmetabolomicsdataimport

7.11 score 15 stars 12 scripts 269 downloads 111 exports 123 dependencies

Last updated 2 months agofrom:f8b70f5c59. Checks:OK: 3 NOTE: 1 ERROR: 3. Indexed: yes.

TargetResultDate
Doc / VignettesOKDec 21 2024
R-4.5-winERRORDec 21 2024
R-4.5-linuxNOTEDec 21 2024
R-4.4-winERRORDec 21 2024
R-4.4-macOKDec 21 2024
R-4.3-winERRORDec 21 2024
R-4.3-macOKDec 21 2024

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.optionsgenericsggplot2ggrepelgluegridExtragsignalgtablehighrhmshtmltoolshtmlwidgetshttrigraphimputeisobanditeratorsitertoolsjquerylibjsonliteknitrlabelinglambda.rlatticelifecyclelimSolvelpSolvemagrittrMASSMassSpecWaveletMatrixmatrixStatsmemoisemgcvmimemissForestmixOmicsmunsellmvtnormnlmeopensslpcaPPpillarpkgconfigplyrpracmaprettyunitsprogresspurrrquadprogR6randomForestrappdirsrARPACKRColorBrewerRcppRcppArmadilloRcppEigenRcppGSLRcppParallelRcppZigguratreadxlrematchreshape2RfastrglrlangrmarkdownrngtoolsRSpectrarvestsassscalesselectrsignalsnowSparseMspeaqstringistringrsystibbletidyrtidyselecttinytexutf8vctrsviridisLitewithrxfunxml2yaml

Introduction to AlpsNMR (older API)

AlpsNMR authors

Rendered fromVig01b-introduction-to-alpsnmr-old-api.Rmdusingknitr::rmarkdownon Dec 21 2024.

Last update: 2024-06-09
Started: 2022-10-14

Introduction to AlpsNMR

AlpsNMR authors

Rendered fromVig01-introduction-to-alpsnmr.Rmdusingknitr::rmarkdownon Dec 21 2024.

Last update: 2024-06-09
Started: 2022-06-15

Handling metadata and annotations

AlpsNMR authors

Rendered fromVig02-handling-metadata-and-annotations.Rmdusingknitr::rmarkdownon Dec 21 2024.

Last update: 2022-06-23
Started: 2022-06-15

Readme and manuals

Help Manual

Help pageTopics
AlpsNMR: Automated spectraL Processing System for NMRAlpsNMR-package AlpsNMR
Extract parts of an nmr_dataset[.nmr_dataset
Extract parts of an nmr_dataset_1D[.nmr_dataset_1D
Extract parts of an nmr_dataset_peak_table[.nmr_dataset_peak_table
K-fold bootstrap and permutation over PLS-VIPbp_kfold_VIP_analysis
Bootstrap and permutation over PLS-VIPbp_VIP_analysis
Download MTBLS242download_MTBLS242
NMR file listerfile_lister
Files to rDoplhinfiles_to_rDolphin
Keep samples based on metadata column criteriafilter.nmr_dataset_family
Format for nmr_datasetformat.nmr_dataset
format for nmr_dataset_1Dformat.nmr_dataset_1D
Format for nmr_dataset_peak_tableformat.nmr_dataset_peak_table
Get integrals with metadata from integrate peak positionsget_integration_with_metadata
The Human Metabolome DataBase multiplet tablehmdb
The Human Metabolome DataBase multiplet table: blood metabolites normally found in NMR-based metabolomicsHMDB_blood
The Human Metabolome DataBase multiplet table: cell metabolites normally found in NMR-based metabolomicsHMDB_cell
The Human Metabolome DataBase multiplet table: urine metabolites normally found in NMR-based metabolomicsHMDB_urine
Object is of nmr_dataset classis.nmr_dataset
Object is of nmr_dataset_1D classis.nmr_dataset_1D
Object is of nmr_dataset_peak_table classis.nmr_dataset_peak_table
nmr_dataset_loadload_and_save_functions nmr_dataset_load nmr_dataset_save
Models stability plotmodels_stability_plot_bootstrap
Models stability plotmodels_stability_plot_plsda
Create an nmr_dataset objectnew_nmr_dataset
Creates a new 1D nmr_dataset object from scratchnew_nmr_dataset_1D
Creates a new nmr_dataset_peak_table object from scratchnew_nmr_dataset_peak_table
Align NMR spectranmr_align
Find alignment referencenmr_align_find_ref
Rephase 1D NMR datanmr_autophase
Estimate the baseline on an nmr_dataset_1D object, using baseline::baseline.als.nmr_baseline_estimation
Baseline Removal NMRnmr_baseline_removal
Threshold estimation for peak detectionnmr_baseline_threshold
Plot the baseline thresholdsnmr_baseline_threshold_plot
Batman helpersnmr_batman nmr_batman_export_dataset nmr_batman_metabolites_list nmr_batman_multi_data_user nmr_batman_multi_data_user_hmdb nmr_batman_write_options
Batman Options helpernmr_batman_options
Build a peak table from the clustered peak listnmr_build_peak_table
Set/Return the full spectra matrixnmr_data nmr_data.nmr_dataset_1D nmr_data<- nmr_data<-.nmr_dataset_1D
Export 1D NMR data to SummarizedExperimentnmr_data_1r_to_SummarizedExperiment
Data analysisnmr_data_analysis
Create method for NMR data analysisnew_nmr_data_analysis_method nmr_data_analysis_method
nmr_dataset (S3 class)nmr_dataset
nmr_dataset_1D (S3 class)nmr_dataset_1D
nmr_dataset like objects (S3 classes)nmr_dataset_family
nmr_dataset_peak_table (S3 class)as.data.frame.nmr_dataset_peak_table nmr_dataset_peak_table
Export nmr_dataset_peak_table to SummarizedExperimentnmr_dataset_peak_table_to_SummarizedExperiment
Peak detection for NMRnmr_detect_peaks
Plot peak detection resultsnmr_detect_peaks_plot
Overview of the peak detection resultsnmr_detect_peaks_plot_overview
Plot multiple peaks from a peak listnmr_detect_peaks_plot_peaks
Diagnose SNR threshold in peak detectionnmr_detect_peaks_tune_snr
Exclude region from samplesnmr_exclude_region nmr_exclude_region.nmr_dataset_1D
Export 1D NMR data to a CSV filenmr_export_data_1r
Compute peak to peak distancesnmr_get_peak_distances
NMR peak identification (plasma/serum samples)nmr_identify_regions_blood
NMR peak identification (cell samples)nmr_identify_regions_cell
NMR peak identification (urine samples)nmr_identify_regions_urine
Integrate peak positionsnmr_integrate_peak_positions
Integrate regionsnmr_integrate_regions nmr_integrate_regions.nmr_dataset_1D
Interpolate a set of 1D NMR Spectranmr_interpolate_1D nmr_interpolate_1D.nmr_dataset
Add metadata to an nmr_dataset objectnmr_meta_add nmr_meta_add_tidy_excel
Export Metadata to an Excel filenmr_meta_export
Get metadatanmr_meta_get
Get a single metadata columnnmr_meta_get_column
Get the names of metadata groupsnmr_meta_groups
Normalize nmr_dataset_1D samplesnmr_normalize nmr_normalize_extra_info
Build a PCA on for an nmr_datasetnmr_pca_build_model nmr_pca_build_model.nmr_dataset_1D
Compute PCA residuals and score distance for each samplenmr_pca_outliers
Exclude outliersnmr_pca_outliers_filter
Plot for outlier detection diagnosticnmr_pca_outliers_plot
Outlier detection through robust PCAnmr_pca_outliers_robust
Plotting functions for PCAnmr_pca_loadingplot nmr_pca_plots nmr_pca_plot_variance nmr_pca_scoreplot
Peak clusteringnmr_peak_clustering
Plot clustering resultsnmr_peak_clustering_plot
PPM resolution of the spectranmr_ppm_resolution nmr_ppm_resolution.nmr_dataset nmr_ppm_resolution.nmr_dataset_1D
Read Free Induction Decay filenmr_read_bruker_fid
Read NMR samplesnmr_read_samples nmr_read_samples_dir
Create one zip file for each brucker sample pathnmr_zip_bruker_samples
to rDolphinParameters_blood
Parameters for cell samples profilingParameters_cell
Parameters for urine samples profilingParameters_urine
Peak detection for NMRPeak_detection
Peak list: Create an 'accepted' column based on some criteriapeaklist_accept_peaks
Fit lorentzians to each peak to estimate areaspeaklist_fit_lorentzians
Permutation testpermutation_test_model
Permutation test plotpermutation_test_plot
PipelinesPipelines pipe_add_metadata pipe_exclude_regions pipe_filter_samples pipe_interpolate_1D pipe_load_samples Pipe_normalization pipe_normalization pipe_outlier_detection pipe_pakdet_align pipe_peakdet_align pipe_peak_integration
Bootstrap plot predictionsplot_bootstrap_multimodel
Plots in WebGLplot_interactive
Multi PLDSA model plot predictionsplot_plsda_multimodel
Plot PLSDA predictionsplot_plsda_samples
Plot vip scores of bootstrapplot_vip_scores
Plot a dataset into a HTML fileplot_webgl
Plot an nmr_dataset_1Dplot.nmr_dataset_1D
Compare PLSDA auroc VIP resultsplsda_auroc_vip_compare
Method for nmr_data_analysis (PLSDA model with AUROC and VIP outputs)plsda_auroc_vip_method
Unlisted PPM resolutionppm_resolution
Print for nmr_datasetprint.nmr_dataset
print for nmr_dataset_1Dprint.nmr_dataset_1D
print for nmr_dataset_peak_tableprint.nmr_dataset_peak_table
Random subsamplingrandom_subsampling
ROIs for blood (plasma/serum) samplesROI_blood
ROIs for cell samplesROI_cell
ROIs for urine samplesROI_urine
Save files to rDoplhinsave_files_to_rDolphin
Save rDoplhin outputsave_profiling_output
Import SummarizedExperiment as 1D NMR dataSummarizedExperiment_to_nmr_data_1r
Import SummarizedExperiment as mr_dataset_peak_tableSummarizedExperiment_to_nmr_dataset_peak_table
Get a tidy data frame from nmr_data objecttidy.nmr_dataset_1D
Export data for the ASICS spectral quantification libraryto_ASICS
Convert to ChemoSpec Spectra classto_ChemoSpec
Validate nmr_dataset objectsvalidate_nmr_dataset validate_nmr_dataset_1D
Validate nmr_dataset_family objectsvalidate_nmr_dataset_family
Validate nmr_dataset_peak_table objectsvalidate_nmr_dataset_peak_table