Package: metabodecon 1.2.6

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_1.2.6.tar.gz
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metabodecon.pdf |metabodecon.html
metabodecon/json (API)
NEWS

# 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 site:https://spang-lab.github.io

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

On CRAN:

nmrdeconvolution

3.48 score 2 stars 2 scripts 299 downloads 60 exports 68 dependencies

Last updated 1 months agofrom:7803136138. Checks:4 OK, 4 ERROR. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKFeb 21 2025
R-4.5-winERRORFeb 21 2025
R-4.5-macOKFeb 21 2025
R-4.5-linuxOKFeb 21 2025
R-4.4-winERRORFeb 21 2025
R-4.4-macOKFeb 21 2025
R-4.3-winERRORFeb 21 2025
R-4.3-macERRORFeb 21 2025

Exports:alignas_decon0as_decon1as_decon2as_decons0as_decons1as_decons2as_ideconas_ideconsas_ispecas_ispecsas_spectraas_spectrumcalculate_lorentz_curvescombine_peaksconvert_posconvert_widthdatadirdatadir_persistentdatadir_tempdeconvolutedohClusterdownload_example_datasetsdraw_spectrumevalwithgen_feat_matgenerate_lorentz_curvesgenerate_lorentz_curves_simget_data_dirget_ppm_rangeis_alignis_alignsis_decon0is_decon1is_decon2is_decons0is_decons1is_decons2is_ideconis_ideconsis_ispecis_ispecsis_spectrais_spectrummake_spectrummetabodecon_fileMetaboDecon1Dplot_lorentz_curves_save_as_pngplot_spectraplot_spectrumplot_spectrum_superposition_save_as_pngplot_tripletsread_spectraread_spectrumsimulate_spectrumspeaq_aligntmpdirtransptreewidth

Dependencies:askpasscliclustercodetoolscolorspacecurldata.tabledigestdoRNGdoSNOWfansifarverforeachggplot2gluegridExtragtablehttrimputeisobanditeratorsitertoolsjsonlitelabelinglatticelifecyclemagrittrMASSMassSpecWaveletmathjaxrMatrixmgcvmimemissForestmunsellnlmeopensslpillarpkgconfigplyrR6randomForestRColorBrewerRcppRcppArmadilloRcppGSLRcppParallelRcppZigguratreadJDXreshape2Rfastrlangrngtoolsrvestscalesselectrsnowspeaqstringistringrsystibbletoscutilutf8vctrsviridisLitewithrxml2

Readme and manuals

Help Manual

Help pageTopics
Align Spectraalign
Convert to a Metabodecon Classas_decon0 as_decon1 as_decon2 as_decons0 as_decons1 as_decons2 as_idecon as_idecons as_ispec as_ispecs as_metabodecon_class as_spectra as_spectrum
Calculate lorentz curves for each analyzed spectrumcalculate_lorentz_curves
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
Deconvolute one or more NMR spectradeconvolute generate_lorentz_curves generate_lorentz_curves_sim
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
Retrieve directory path of an example datasetget_data_dir
Get PPM Range covered by Spectraget_ppm_range
Is an Object from a Metabodecon Class?is_align is_aligns is_decon0 is_decon1 is_decon2 is_decons0 is_decons1 is_decons2 is_idecon is_idecons is_ispec is_ispecs is_metabodecon_class is_spectra is_spectrum
Create a Spectrum Objectmake_spectrum
Metabodecon Classesmetabodecon_classes
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.idecon print.idecons print.ispec print.ispecs 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
Calculate the Width of a Numeric Vectorwidth