Package description | Quick overview of main functions | References
Package: ASICS 2.29.0
Gaëlle Lefort
ASICS: Automatic Statistical Identification in Complex Spectra
With a set of pure metabolite reference spectra, ASICS quantifies concentration of metabolites in a complex spectrum. The identification of metabolites is performed by fitting a mixture model to the spectra of the library with a sparse penalty. The method and its statistical properties are described in Tardivel et al. (2017) <doi:10.1007/s11306-017-1244-5>.
Authors:
ASICS_2.29.0.tar.gz
ASICS_2.29.0.zip(r-4.7)ASICS_2.29.0.zip(r-4.6)ASICS_2.29.0.zip(r-4.5)
ASICS_2.29.0.tgz(r-4.6-any)ASICS_2.29.0.tgz(r-4.5-any)
ASICS_2.29.0.tar.gz(r-4.7-any)ASICS_2.29.0.tar.gz(r-4.6-any)
ASICS_2.29.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
ASICS/json (API)
| # Install 'ASICS' in R: |
| install.packages('ASICS', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Datasets:
- pure_library - Pure spectra library
On BioConductor:ASICS-2.29.0(bioc 3.24)ASICS-2.28.0(bioc 3.23)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
softwaredataimportcheminformaticsmetabolomics
Last updated from:1d197eb2ea. Checks:8 WARNING, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | WARNING | 214 | ||
| linux-devel-x86_64 | WARNING | 589 | ||
| source / vignettes | OK | 385 | ||
| linux-release-x86_64 | WARNING | 572 | ||
| macos-release-arm64 | WARNING | 526 | ||
| macos-oldrel-arm64 | WARNING | 371 | ||
| windows-devel | WARNING | 492 | ||
| windows-release | WARNING | 532 | ||
| windows-oldrel | WARNING | 472 | ||
| wasm-release | OK | 212 |
Exports:alignSpectraASICSASICSUsersGuidebinningcreatePureLibrarycreateSpectraformatForAnalysisgetBestModelgetCVErrorgetDatasetgetDeformedLibrarygetMeanByGroupgetNbProtonsgetNormMethodgetNormParamsgetPpmGridgetQuantificationgetReconstructedSpectragetResultsgetSampleNamegetSpectragetTypeAnalysisgetTypeDataimportSpectraimportSpectraBrukerkruskalWallisnormaliseSpectraoplsdapcaplotplotAlignmentshowsimulate_spectrasummary
Dependencies:abindaskpassbase64encBHBiobaseBiocBaseUtilsBiocGenericsBiocParallelbslibcachemcalibrateclicodetoolscpp11crosstalkcurldata.tableDelayedArraydigestdplyrevaluatefarverfastmapfontawesomeforeachformatRfsfutile.loggerfutile.optionsgenericsGenomicRangesggplot2ggrepelglmnetgluegridExtragtablehighrhtmltoolshtmlwidgetshttrIRangesisobanditeratorsjquerylibjsonliteknitrlabelinglambda.rlaterlatticelazyevallifecyclelimmamagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemimeMultiAssayExperimentMultiDataSetmvtnormopensslotelPepsNMRpillarpkgconfigplotlyplyrpromisesptwpurrrqqmanquadprogR6rappdirsRColorBrewerRcppRcppArmadilloRcppDERcppEigenreshape2rlangrmarkdownroplsS4ArraysS4VectorsS7sassscalesSeqinfoshapesnowSparseArraystatmodstringistringrSummarizedExperimentsurvivalsystibbletidyrtidyselecttinytexutf8vctrsviridisLitewithrxfunXVectoryamlzoo
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Accessors | accessors-methods getBestModel getBestModel,AnalysisResults-method getCVError getCVError,AnalysisResults-method getDataset getDataset,AnalysisResults-method getDeformedLibrary getDeformedLibrary,ASICSResults-method getMeanByGroup getMeanByGroup,AnalysisResults-method getNbProtons getNbProtons,PureLibrary-method getNormMethod getNormMethod,Spectra-method getNormParams getNormParams,Spectra-method getPpmGrid getPpmGrid,Spectra-method getQuantification getQuantification,ASICSResults-method getReconstructedSpectra getReconstructedSpectra,ASICSResults-method getResults getResults,AnalysisResults-method getSampleName getSampleName,Spectra-method getSpectra getSpectra,Spectra-method getTypeAnalysis getTypeAnalysis,AnalysisResults-method getTypeData getTypeData,AnalysisResults-method |
| Alignment | alignSpectra |
| Class AnalysisResults | AnalysisResults-class |
| Automatic Statistical Identification in Complex Spectra | ASICS |
| Class ASICSResults | ASICSResults-class |
| View ASICS User's Guide | ASICSUsersGuide |
| Binning/Bucketing of NMR spectra | binning |
| Combine or subset functions | c,ASICSResults-method c,PureLibrary-method c,Spectra-method c.ASICSResults c.PureLibrary c.Spectra combineAndSubset-methods [,ASICSResults,ANY,ANY,ANY-method [,PureLibrary,ANY,ANY,ANY-method [,Spectra,ANY,ANY,ANY-method [.ASICSResults [.PureLibrary [.Spectra |
| Create a pure library | createPureLibrary |
| Create a Spectra object | createSpectra |
| Format data for analysis | formatForAnalysis |
| Import metabolomic spectra | importSpectra |
| Import preprocessed metabolomic spectra from Bruker files | importSpectraBruker |
| Kruskal-Wallis rank sum tests on a 'SummarizedExperiment' object | kruskalWallis |
| Normalisation | normaliseSpectra |
| Orthogonal projections to latent structures discriminant analysis (OPLS-DA) on a 'SummarizedExperiment' object | oplsda |
| Principal Component Analysis (PCA) on a 'SummarizedExperiment' object | pca |
| Tile plot | plotAlignment |
| Pure spectra library | pure_library |
| Class 'PureLibrary' | PureLibrary-class |
| Simulate a set of spectra | simulate_spectra |
| Class Spectra | Spectra-class |
| Summary methods | dim,ASICSResults-method dim,Spectra-method dim.Spectra length,Spectra-method length.Spectra show,AnalysisResults-method show,ASICSResults-method show,Spectra-method show.AnalysisResults show.ASICSResults show.Spectra summary,AnalysisResults-method summary,Spectra-method summary-methods summary.AnalysisResults summary.Spectra |
| Visualisation methods | plot,AnalysisResults,ANY-method plot.AnalysisResults visualisation-methods-analyses |
| Visualisation methods | plot,ASICSResults,ANY-method plot,Spectra,ANY-method plot.ASICSResults plot.Spectra visualisation-methods-spectra |