Package: metabodecon 1.7.0

Tobias Schmidt

metabodecon: Deconvolution and Alignment of 1d NMR Spectra

A framework for deconvolution, alignment and postprocessing of 1-dimensional (1d) nuclear magnetic resonance (NMR) spectra, resulting in a data matrix of aligned signal integrals. The deconvolution part uses the algorithm described in Koh et al. (2009) <doi:10.1016/j.jmr.2009.09.003>. The alignment part is based on functions from the 'speaq' package, described in Beirnaert et al. (2018) <doi:10.1371/journal.pcbi.1006018> and Vu et al. (2011) <doi:10.1186/1471-2105-12-405>. A detailed description and evaluation of an early version of the package, 'MetaboDecon1D v0.2.2', can be found in Haeckl et al. (2021) <doi:10.3390/metabo11070452>.

Authors:Tobias Schmidt [aut, cre, cph], Martina Haeckl [aut, cph], Yanren Linda Hu [ctb], Wolfram Gronwald [aut, cph]

metabodecon_1.7.0.tar.gz
metabodecon_1.7.0.zip(r-4.7)metabodecon_1.7.0.zip(r-4.6)metabodecon_1.7.0.zip(r-4.5)
metabodecon_1.7.0.tgz(r-4.6-any)metabodecon_1.7.0.tgz(r-4.5-any)
metabodecon_1.7.0.tar.gz(r-4.7-any)metabodecon_1.7.0.tar.gz(r-4.6-any)
metabodecon_1.7.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
metabodecon/json (API)

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

Bug tracker:https://github.com/spang-lab/metabodecon/issues

Pkgdown/docs site:https://spang-lab.github.io

Datasets:
  • sap - The SAP Dataset
  • sim - The Sim Dataset

On CRAN:

Conda:

nmrdeconvolution

5.18 score 5 stars 7 scripts 165 downloads 66 exports 67 dependencies

Last updated from:46060c075b. Checks:9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-x86_64OK190
source / vignettesOK259
linux-release-x86_64OK193
macos-release-arm64OK152
macos-oldrel-arm64OK148
windows-develOK152
windows-releaseOK149
windows-oldrelOK123
wasm-releaseOK152

Exports:aaa_Get_Startedalignas_decon0as_decon1as_decon2as_decons0as_decons1as_decons2as_spectraas_spectrumbenchmark_mdmcalculate_lorentz_curvescheck_mdrbcheck_mdrb_depscombine_peaksconvert_posconvert_widthcv_mdmdatadirdatadir_persistentdatadir_tempdecon_cachedirdeconvolutedohClusterdownload_example_datasetsdraw_spectrumevalwithfit_mdmgen_feat_matgenerate_lorentz_curvesgenerate_lorentz_curves_simget_data_dirget_namesget_pgridget_ppm_rangeget_si_matget_startedheadtailinstall_mdrbis_alignis_alignsis_decon0is_decon1is_decon2is_decons0is_decons1is_decons2is_spectrais_spectrummake_spectrummetabodecon_fileMetaboDecon1Dplot_lorentz_curves_save_as_pngplot_spectraplot_spectrumplot_spectrum_superposition_save_as_pngplot_tripletsread_spectraread_spectrumsimulate_spectrumspeaq_aligntmpdirtransptreetree_previewwidth

Dependencies:askpasscliclustercodetoolscpp11curldata.tabledigestdoRNGdoSNOWfarverforeachggplot2gluegridExtragtablehttrimputeisobanditeratorsitertoolsjsonlitelabelinglatticelifecyclemagrittrMassSpecWaveletmathjaxrMatrixmimemissForestopensslpillarpkgconfigplyrR6randomForestrangerrbibutilsRColorBrewerRcppRcppArmadilloRcppEigenRcppParallelRdpackreadJDXreshape2RfastrlangrngtoolsrvestS7scalesselectrsnowspeaqstringistringrsystibbletoscutilutf8vctrsviridisLitewithrxml2zigg

Get Started
Deconvolute spectra | Visualize deconvoluted spectra | Align deconvoluted spectra
Rendered fromGet_Started.Rmdusingknitr::rmarkdown

Last update: 2026-04-10
Started: 2025-01-15

Metabodecon Models
Simulate spectra | Train/test split | Fit a single model | Tune preprocessing via grid search | Compare deconvolution results | Inspect lasso features | Predict test samples | Benchmark with nested cross-validation
Rendered fromMDM.Rmdusingknitr::rmarkdown

Last update: 2026-04-10
Started: 2026-04-10

Readme and manuals

Help Manual

Help pageTopics
Get URL of Metabodecon "Get Started" Pageaaa_Get_Started get_started
Align Spectraalign
Convert to a Metabodecon Objectas_decon0 as_decon1 as_decon2 as_decons0 as_decons1 as_decons2 as_metabodecon_class as_spectra as_spectrum
Calculate lorentz curves for each analyzed spectrumcalculate_lorentz_curves
Check Rust Backend Requirementscheck_mdrb check_mdrb_deps
Combine Peakscombine_peaks
Convert from unit A to unit Bconvert_pos convert_width
Return path to metabodecon's data directorydatadir
Persistent Data Directorydatadir_persistent
Temporary Data Directorydatadir_temp
Get Default Cache Directory for Deconvolutiondecon_cachedir
Deconvolute one or more NMR spectradeconvolute
Cluster Based Peak AlignmentdohCluster
Download metabodecon Example Datasetsdownload_example_datasets
Draw Spectrumdraw_spectrum
Evaluate an expression with predefined global stateevalwith
Generate Feature Matrix.gen_feat_mat
Deconvolute one or more NMR spectragenerate_lorentz_curves generate_lorentz_curves_sim
Retrieve directory path of an example datasetget_data_dir
Returns the names of a metabodecon collection object.get_names
Get PPM Range covered by Spectraget_ppm_range
Extract Matrix of aligned Signal Intensitiesget_si_mat
Show head and tail rows of a matrix-like objectheadtail
Install Rust Backendinstall_mdrb
Is an Object from a Metabodecon Class?is_align is_aligns is_decon0 is_decon1 is_decon2 is_decons0 is_decons1 is_decons2 is_metabodecon_class is_spectra is_spectrum
Create a Spectrum Objectmake_spectrum
Metabodecon Modelsbenchmark_mdm cv_mdm fit_mdm get_pgrid mdm
S3 methods for mdm objectscoef.mdm mdm_methods plot.mdm predict.mdm print.mdm print.summary.mdm summary.mdm
Return Path to File or Directory in metabodecon Packagemetabodecon_file
Deconvolute 1D NMR spectrumMetaboDecon1D
Plot lorentz curves for variable rangeplot_lorentz_curves_save_as_png
Plot Spectraplot_spectra
Plot Spectrumplot_spectrum
Plot spectrum approx for variable rangeplot_spectrum_superposition_save_as_png
Plot peak triplets for variable rangeplot_triplets
S3 Methods for Printing Metabodecon Objectsprint.align print.aligns print.decon1 print.decon2 print.decons1 print.decons2 print.spectra print.spectrum print_methods
Read one or more spectra from Diskread_spectra
Read one or more spectra from Diskread_spectrum
The SAP Datasetsap
The Sim Datasetsim
Simulate a 1D NMR Spectrumsimulate_spectrum
Align Signals using 'speaq'speaq_align
Temporary Session Directorytmpdir
Make transparenttransp
Print the Structure of a Directory Treetree tree_preview
Calculate the Width of a Numeric Vectorwidth