Package: PepsNMR 1.30.0

Manon Martin

PepsNMR: Pre-process 1H-NMR FID signals

This package provides R functions for common pre-procssing steps that are applied on 1H-NMR data. It also provides a function to read the FID signals directly in the Bruker format.

Authors:Manon Martin [aut, cre], Bernadette Govaerts [aut, ths], Benoît Legat [aut], Paul H.C. Eilers [aut], Pascal de Tullio [dtc], Bruno Boulanger [ctb], Julien Vanwinsberghe [ctb]

PepsNMR_1.30.0.tar.gz
PepsNMR_1.30.0.zip(r-4.7)PepsNMR_1.30.0.zip(r-4.6)PepsNMR_1.30.0.zip(r-4.5)
PepsNMR_1.30.0.tgz(r-4.6-any)PepsNMR_1.30.0.tgz(r-4.5-any)
PepsNMR_1.30.0.tar.gz(r-4.7-any)PepsNMR_1.30.0.tar.gz(r-4.6-any)
PepsNMR_1.30.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
PepsNMR/json (API)

# Install 'PepsNMR' in R:

install.packages('PepsNMR', repos = c('https://bioc-release.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/manonmartin/pepsnmr/issues

On BioConductor:PepsNMR-1.31.0(bioc 3.24)PepsNMR-1.30.0(bioc 3.23)

software preprocessing visualization metabolomics dataimport

6.52 score 8 stars 1 packages 23 scripts 465 downloads 2 mentions 22 exports 30 dependencies

Last updated from:64208a8046 (on RELEASE_3_23). Checks:1 WARNING, 7 NOTE, 2 OK. Indexed: no.

Target	Result	Time
bioc-checks	WARNING	181
linux-devel-x86_64	NOTE	454
source / vignettes	OK	286
linux-release-x86_64	NOTE	442
macos-release-arm64	NOTE	259
macos-oldrel-arm64	NOTE	270
windows-devel	NOTE	589
windows-release	NOTE	668
windows-oldrel	NOTE	523
wasm-release	OK	119

Exports:Apodization BaselineCorrection Bucketing Draw DrawPCA DrawSignal FirstOrderPhaseCorrection FourierTransform GroupDelayCorrection InternalReferencing NegativeValuesZeroing Normalization PreprocessingChain ReadFid ReadFids RegionRemoval SolventSuppression Warping WindowSelection ZeroFilling ZeroOrderPhaseCorrection ZoneAggregation

Dependencies:cli cpp11 farver ggplot2 glue gridExtra gtable isoband labeling lattice lifecycle magrittr Matrix matrixStats plyr ptw R6 RColorBrewer Rcpp RcppArmadillo RcppDE reshape2 rlang S7 scales stringi stringr vctrs viridisLite withr

Application of PepsNMR on the Human Serum dataset

Rendered fromPepsNMR_minimal_example.Rmdusingknitr::rmarkdown

Last update: 2019-12-08
Started: 2018-01-15

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Metabolomic data pre-processing strategy for 1H NMR spectroscopic data	PepsNMR-package PepsNMR
Apodization of the FID	Apodization
Set the baseline to a uniform zero signal.	BaselineCorrection
Spectral data reduction	Bucketing
Draw signals or their PCA scores/loadings.	Draw
Draw the PCA scores or loadings of the signals	DrawPCA
Draw Signals	DrawSignal
Perform a first order phase correction.	FirstOrderPhaseCorrection
Applies the fourier transforationm to the FIDs.	FourierTransform
Perform a first order phase correction.	GroupDelayCorrection
Chemical shift referencing.	InternalReferencing
Zeroing of negative values.	NegativeValuesZeroing
Normalizes the spectra	Normalization
Proprocessing workflow for 1H-NMR data	PreprocessingChain
Read FIDs in Bruker format from a directory	ReadFids
Removal of non-informative regions	RegionRemoval
Suppress the Solvent signal present in each FID.	SolventSuppression
Warping of the spectra	Warping
Spectral window selection	WindowSelection
Zero Filling	ZeroFilling
Zero Order Phase Correction	ZeroOrderPhaseCorrection
Aggregates the values in a given ppm interval.	ZoneAggregation