Man pages for sipss/AlpsNMR
Automated spectraL Processing System for NMR

AlpsNMR-packageAlpsNMR: Automated spectraL Processing System for NMR
bp_kfold_VIP_analysisK-fold bootstrap and permutation over PLS-VIP
bp_VIP_analysisBootstrap and permutation over PLS-VIP
download_MTBLS242Download MTBLS242
file_listerNMR file lister
files_to_rDolphinFiles to rDoplhin
filter.nmr_dataset_familyKeep samples based on metadata column criteria
format.nmr_datasetFormat for nmr_dataset
format.nmr_dataset_1Dformat for nmr_dataset_1D
format.nmr_dataset_peak_tableFormat for nmr_dataset_peak_table
get_integration_with_metadataGet integrals with metadata from integrate peak positions
hmdbThe Human Metabolome DataBase multiplet table
HMDB_bloodThe Human Metabolome DataBase multiplet table: blood...
HMDB_cellThe Human Metabolome DataBase multiplet table: cell...
HMDB_urineThe Human Metabolome DataBase multiplet table: urine...
is.nmr_datasetObject is of nmr_dataset class
is.nmr_dataset_1DObject is of nmr_dataset_1D class
is.nmr_dataset_peak_tableObject is of nmr_dataset_peak_table class
load_and_save_functionsnmr_dataset_load
models_stability_plot_bootstrapModels stability plot
models_stability_plot_plsdaModels stability plot
new_nmr_datasetCreate an nmr_dataset object
new_nmr_dataset_1DCreates a new 1D nmr_dataset object from scratch
new_nmr_dataset_peak_tableCreates a new nmr_dataset_peak_table object from scratch
nmr_alignAlign NMR spectra
nmr_align_find_refFind alignment reference
nmr_autophaseRephase 1D NMR data
nmr_baseline_estimationEstimate the baseline on an nmr_dataset_1D object, using...
nmr_baseline_removalBaseline Removal NMR
nmr_baseline_thresholdThreshold estimation for peak detection
nmr_baseline_threshold_plotPlot the baseline thresholds
nmr_batmanBatman helpers
nmr_batman_optionsBatman Options helper
nmr_build_peak_tableBuild a peak table from the clustered peak list
nmr_dataSet/Return the full spectra matrix
nmr_data_1r_to_SummarizedExperimentExport 1D NMR data to SummarizedExperiment
nmr_data_analysisData analysis
nmr_data_analysis_methodCreate method for NMR data analysis
nmr_datasetnmr_dataset (S3 class)
nmr_dataset_1Dnmr_dataset_1D (S3 class)
nmr_dataset_familynmr_dataset like objects (S3 classes)
nmr_dataset_peak_tablenmr_dataset_peak_table (S3 class)
nmr_dataset_peak_table_to_SummarizedExperimentExport nmr_dataset_peak_table to SummarizedExperiment
nmr_detect_peaksPeak detection for NMR
nmr_detect_peaks_plotPlot peak detection results
nmr_detect_peaks_plot_overviewOverview of the peak detection results
nmr_detect_peaks_plot_peaksPlot multiple peaks from a peak list
nmr_detect_peaks_tune_snrDiagnose SNR threshold in peak detection
nmr_exclude_regionExclude region from samples
nmr_export_data_1rExport 1D NMR data to a CSV file
nmr_get_peak_distancesCompute peak to peak distances
nmr_identify_regions_bloodNMR peak identification (plasma/serum samples)
nmr_identify_regions_cellNMR peak identification (cell samples)
nmr_identify_regions_urineNMR peak identification (urine samples)
nmr_integrate_peak_positionsIntegrate peak positions
nmr_integrate_regionsIntegrate regions
nmr_interpolate_1DInterpolate a set of 1D NMR Spectra
nmr_meta_addAdd metadata to an nmr_dataset object
nmr_meta_exportExport Metadata to an Excel file
nmr_meta_getGet metadata
nmr_meta_get_columnGet a single metadata column
nmr_meta_groupsGet the names of metadata groups
nmr_normalizeNormalize nmr_dataset_1D samples
nmr_pca_build_modelBuild a PCA on for an nmr_dataset
nmr_pca_outliersCompute PCA residuals and score distance for each sample
nmr_pca_outliers_filterExclude outliers
nmr_pca_outliers_plotPlot for outlier detection diagnostic
nmr_pca_outliers_robustOutlier detection through robust PCA
nmr_pca_plotsPlotting functions for PCA
nmr_peak_clusteringPeak clustering
nmr_peak_clustering_plotPlot clustering results
nmr_ppm_resolutionPPM resolution of the spectra
nmr_read_bruker_fidRead Free Induction Decay file
nmr_read_samplesRead NMR samples
nmr_zip_bruker_samplesCreate one zip file for each brucker sample path
Parameters_bloodto rDolphin
Parameters_cellParameters for cell samples profiling
Parameters_urineParameters for urine samples profiling
Peak_detectionPeak detection for NMR
peaklist_accept_peaksPeak list: Create an 'accepted' column based on some criteria
peaklist_fit_lorentziansFit lorentzians to each peak to estimate areas
permutation_test_modelPermutation test
permutation_test_plotPermutation test plot
PipelinesPipelines
plot_bootstrap_multimodelBootstrap plot predictions
plot_interactivePlots in WebGL
plot.nmr_dataset_1DPlot an nmr_dataset_1D
plot_plsda_multimodelMulti PLDSA model plot predictions
plot_plsda_samplesPlot PLSDA predictions
plot_vip_scoresPlot vip scores of bootstrap
plot_webglPlot a dataset into a HTML file
plsda_auroc_vip_compareCompare PLSDA auroc VIP results
plsda_auroc_vip_methodMethod for nmr_data_analysis (PLSDA model with AUROC and VIP...
ppm_resolutionUnlisted PPM resolution
print.nmr_datasetPrint for nmr_dataset
print.nmr_dataset_1Dprint for nmr_dataset_1D
print.nmr_dataset_peak_tableprint for nmr_dataset_peak_table
random_subsamplingRandom subsampling
read_bruker_pdataRead processed Bruker NMR data
reexportsObjects exported from other packages
ROI_bloodROIs for blood (plasma/serum) samples
ROI_cellROIs for cell samples
ROI_urineROIs for urine samples
save_files_to_rDolphinSave files to rDoplhin
save_profiling_outputSave rDoplhin output
sub-.nmr_datasetExtract parts of an nmr_dataset
sub-.nmr_dataset_1DExtract parts of an nmr_dataset_1D
sub-.nmr_dataset_peak_tableExtract parts of an nmr_dataset_peak_table
SummarizedExperiment_to_nmr_data_1rImport SummarizedExperiment as 1D NMR data
SummarizedExperiment_to_nmr_dataset_peak_tableImport SummarizedExperiment as mr_dataset_peak_table
tidy.nmr_dataset_1DGet a tidy data frame from nmr_data object
to_ASICSExport data for the ASICS spectral quantification library
to_ChemoSpecConvert to ChemoSpec Spectra class
validate_nmr_datasetValidate nmr_dataset objects
validate_nmr_dataset_familyValidate nmr_dataset_family objects
validate_nmr_dataset_peak_tableValidate nmr_dataset_peak_table objects
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sipss/AlpsNMR documentation built on Aug. 13, 2024, 5:11 p.m.