Package: MetabolomicsBasics 1.4.5
MetabolomicsBasics: Basic Functions to Investigate Metabolomics Data Matrices
A set of functions to investigate raw data from (metabol)omics experiments intended to be used on a raw data matrix, i.e. following peak picking and signal deconvolution. Functions can be used to normalize data, detect biomarkers and perform sample classification. A detailed description of best practice usage may be found in the publication <doi:10.1007/978-1-4939-7819-9_20>.
Authors:
MetabolomicsBasics_1.4.5.tar.gz
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MetabolomicsBasics.pdf |MetabolomicsBasics.html✨
MetabolomicsBasics/json (API)
| # Install 'MetabolomicsBasics' in R: |
| install.packages('MetabolomicsBasics', repos = c('https://janlisec.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/janlisec/metabolomicsbasics/issues
Last updated 9 months agofrom:6037c8182a. Checks:OK: 5 NOTE: 2. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Oct 27 2024 |
| R-4.5-win | OK | Sep 27 2024 |
| R-4.5-linux | OK | Oct 27 2024 |
| R-4.4-win | NOTE | Oct 27 2024 |
| R-4.4-mac | NOTE | Oct 27 2024 |
| R-4.3-win | OK | Oct 27 2024 |
| R-4.3-mac | OK | Oct 27 2024 |
Exports:AdjustSymbolsCheckForOutliersClassificationCVClassificationHistogramClassificationWrapperfind_boundariesMBoxplotMetaboliteANOVAmsconvertPlotMetabolitePCAPlotPValueHistPolarCoordHeterPlotRemoveFactorsByANOVAReplaceMissingValuesRestrictedPCAspectra_format_convertersumformula_from_CASunique_labelsunique_subformula_masses
Dependencies:askpassbase64encBiobaseBiocGenericsC50caretclasscliclockcodetoolscolorspacecpp11Cubistcurldata.tabledata.treediagramdigestdplyre1071enviPatfansifarverforeachFormulafuturefuture.applygenericsggplot2globalsgluegowergtablehardhathttrInterpretMSSpectruminumipredisobanditeratorsjsonliteKernSmoothlabelinglatticelavalibcoinlifecyclelistenvlubridatemagrittrMASSMatrixmgcvmimeModelMetricsmunsellmvtnormnlmennetnumDerivopensslparallellypartykitpcaMethodspillarpkgconfigplyrpROCprodlimprogressrproxypurrrR6RColorBrewerRcpprecipesreshape2rlangrpartrvestscalesselectrshapeSQUAREMstringistringrsurvivalsystibbletidyrtidyselecttimechangetimeDatetzdbutf8vctrsviridisLitewebchemwithrxml2
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| AdjustSymbols. | AdjustSymbols |
| CheckForOutliers. | CheckForOutliers |
| ClassificationCV. | ClassificationCV |
| ClassificationHistogram. | ClassificationHistogram |
| ClassificationWrapper. | ClassificationWrapper |
| find_boundaries. | find_boundaries |
| MBoxplot. | MBoxplot |
| Metabolite table | met |
| MetaboliteANOVA. | MetaboliteANOVA |
| msconvert. | msconvert |
| PlotMetabolitePCA. | PlotMetabolitePCA |
| PlotPValueHist. | PlotPValueHist |
| PolarCoordHeterPlot. | PolarCoordHeterPlot |
| Metabolomics data set | raw |
| RemoveFactorsByANOVA. | RemoveFactorsByANOVA |
| ReplaceMissingValues. | ReplaceMissingValues |
| RestrictedPCA. | RestrictedPCA |
| Sample table | sam |
| spectra_format_converter. | spectra_format_converter |
| sumformula_from_CAS. | sumformula_from_CAS |
| unique_labels. | unique_labels |
| unique_subformula_masses | unique_subformula_masses |
