Package: speaq 2.7.0

speaq: Tools for Nuclear Magnetic Resonance (NMR) Spectra Alignment, Peak Based Processing, Quantitative Analysis and Visualizations

Makes Nuclear Magnetic Resonance spectroscopy (NMR spectroscopy) data analysis as easy as possible by only requiring a small set of functions to perform an entire analysis. 'speaq' offers the possibility of raw spectra alignment and quantitation but also an analysis based on features whereby the spectra are converted to peaks which are then grouped and turned into features. These features can be processed with any number of statistical tools either included in 'speaq' or available elsewhere on CRAN. More details can be found in Vu et al. (2011) <doi:10.1186/1471-2105-12-405> and Beirnaert et al. (2018) <doi:10.1371/journal.pcbi.1006018>.

Authors:Charlie Beirnaert, Trung Nghia Vu, Pieter Meysman, Kris Laukens and Dirk Valkenborg

speaq_2.7.0.tar.gz
speaq_2.7.0.zip(r-4.5)speaq_2.7.0.zip(r-4.4)speaq_2.7.0.zip(r-4.3)
speaq_2.7.0.tgz(r-4.4-any)speaq_2.7.0.tgz(r-4.3-any)
speaq_2.7.0.tar.gz(r-4.5-noble)speaq_2.7.0.tar.gz(r-4.4-noble)
speaq_2.7.0.tgz(r-4.4-emscripten)speaq_2.7.0.tgz(r-4.3-emscripten)
speaq.pdf |speaq.html✨
speaq/json (API)
NEWS

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

Peer review:

Bug tracker:https://github.com/beirnaert/speaq/issues

Datasets:

On CRAN:

6.55 score 9 stars 1 packages 26 scripts 418 downloads 5 mentions 29 exports 64 dependencies

Last updated 3 years agofrom:3fa92499b7. Checks:OK: 3 NOTE: 4. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 25 2024
R-4.5-winNOTEOct 25 2024
R-4.5-linuxNOTEOct 25 2024
R-4.4-winNOTEOct 25 2024
R-4.4-macNOTEOct 25 2024
R-4.3-winOKOct 25 2024
R-4.3-macOKOct 25 2024

Exports:AddPlottingStuffBuildFeatureMatrixBuildRawDataMatrixBWRcreateNullSamplingdetectSpecPeaksdohClusterdohClusterCustommedSegmentsdoShiftdrawBWdrawSpecdrawSpecPPMfindReffindSegPeakListfindShiftStepFFTgetWaveletPeaksGetWinedata.subsethclust.groupinghClustAlignHMDBsearchRmakeSimulatedDataPeakFillingPeakGrouperregroupRrelevant.features.preturnLocalMaximaROIplotSCANTSilhouetR

Dependencies:askpasscliclustercodetoolscolorspacecurldata.tabledigestdoRNGdoSNOWfansifarverforeachggplot2gluegridExtragtablehttrimputeisobanditeratorsitertoolsjsonlitelabelinglatticelifecyclemagrittrMASSMassSpecWaveletMatrixmgcvmimemissForestmunsellnlmeopensslpillarpkgconfigplyrR6randomForestRColorBrewerRcppRcppArmadilloRcppGSLRcppParallelRcppZigguratreshape2Rfastrlangrngtoolsrvestscalesselectrsnowstringistringrsystibbleutf8vctrsviridisLitewithrxml2

User guide for speaq package version <= 1.2.3

Trung Nghia Vu, Charlie Beirnaert, et al.

Rendered fromclassic_speaq_vignette.Rmdusingknitr::rmarkdownon Oct 25 2024.

Last update: 2018-11-20
Started: 2017-05-11

speaq 2.0 function illustrations

Charlie Beirnaert

Rendered fromspeaq2_illustrations.Rmdusingknitr::rmarkdownon Oct 25 2024.

Last update: 2019-02-22
Started: 2017-05-09

Readme and manuals

Help Manual

Help pageTopics
Add plotting variablesAddPlottingStuff
Build a Feature matrix from the with speaq 2.0 processed dataBuildFeatureMatrix
Build a raw data matrix (spectra) from spectra of unequal lengthBuildRawDataMatrix
BW ratio calculationBWR
Building a null hypothesis datacreateNullSampling
Peak detection for spectradetectSpecPeaks
CluPA function for multiple spectra.dohCluster
Use CluPA for alignment with additional informationdohClusterCustommedSegments
Segment shiftdoShift
BW and percentile ratios plotdrawBW
Spectral plotdrawSpec
Plot NMR spectra from a spectra data matrixdrawSpecPPM
Reference findingfindRef
Selecting the peaks in a segmentfindSegPeakList
Finding the shift-step by using Fast Fourier Transform cross- correlationfindShiftStepFFT
Convert raw NMR spectra to peak data by using waveletsgetWaveletPeaks
Get subset of Winedata for code examplesGetWinedata.subset
Grouping with hierarchical clustering (used in the PeakGrouper function)hclust.grouping
CluPA function for two spectra.hClustAlign
Submit 1H NMR peaks to HMDB for compound searchHMDBsearchR
Create a simulated NMR spectral datamakeSimulatedData
Peak filling of any missed peaksPeakFilling
Peak grouping with hierarchical clusteringPeakGrouper
Regroup faulty grouped peaksregroupR
Identify features (columns in the datamatrix) which are significantly associated with the outcome.relevant.features.p
Local maximum detectionreturnLocalMaxima
Plot NMR spectra, together with raw and grouped peaksROIplot
SCAle, Normalize and Transform a data matrixSCANT
SilhouetRSilhouetR
Wine datasetWinedata