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MsCoreUtils

Core Utils for Mass Spectrometry Data

Bioconductor version: 3.24 · Package version: 1.25.4

MsCoreUtils defines low-level functions for mass spectrometry data and is independent of any high-level data structures. These functions include mass spectra processing functions (noise estimation, smoothing, binning, baseline estimation), quantitative aggregation functions (median polish, robust summarisation, ...), missing data imputation, data normalisation (quantiles, vsn, ...), misc helper functions, that are used across high-level data structure within the R for Mass Spectrometry packages.

Installation

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("MsCoreUtils")

Details

MaintainerRforMassSpectrometry Package Maintainer <maintainer@rformassspectrometry.org>
AuthorRforMassSpectrometry Package Maintainer [cre], Laurent Gatto [aut] (ORCID: <https://orcid.org/0000-0002-1520-2268>), Johannes Rainer [aut] (ORCID: <https://orcid.org/0000-0002-6977-7147>), Sebastian Gibb [aut] (ORCID: <https://orcid.org/0000-0001-7406-4443>), Philippine Louail [aut] (ORCID: <https://orcid.org/0009-0007-5429-6846>), Adriano Rutz [aut] (ORCID: <https://orcid.org/0000-0003-0443-9902>), Adriaan Sticker [ctb], Sigurdur Smarason [ctb], Thomas Naake [ctb], Josep Maria Badia Aparicio [ctb] (ORCID: <https://orcid.org/0000-0002-5704-1124>), Michael Witting [ctb] (ORCID: <https://orcid.org/0000-0002-1462-4426>), Samuel Wieczorek [ctb], Roger Gine Bertomeu [ctb] (ORCID: <https://orcid.org/0000-0003-0288-9619>), Mar Garcia-Aloy [ctb] (ORCID: <https://orcid.org/0000-0002-1330-6610>), Gabriele Tomè [ctb] (ORCID: <https://orcid.org/0000-0002-3976-6068>), Muyao Xi [ctb]
LicenseArtistic-2.0
URLhttps://github.com/RforMassSpectrometry/MsCoreUtils
Bug Reportshttps://github.com/RforMassSpectrometry/MsCoreUtils/issues
Downloads rank4732
Source branchdevel
biocViewsInfrastructure, MassSpectrometry, Metabolomics, Proteomics, Software

Documentation

Download

Follow the installation instructions to use this package in your R session.

Source packageMsCoreUtils_1.25.4.tar.gz
Windows binary (x86_64)MsCoreUtils_1.25.4.zip
macOS binary (arm64)MsCoreUtils_1.25.4.tgz
macOS binary (x86_64)MsCoreUtils_1.25.4.tgz
Dependencies

Depends: R (>= 3.6.0)

Imports: methods, S4Vectors, MASS, stats, clue

LinkingTo: Rcpp

Suggests: testthat, knitr, BiocStyle, rmarkdown, roxygen2, imputeLCMD, impute, norm, pcaMethods, vsn, Matrix, preprocessCore, missForest, rlang

Enhances: HDF5Array

Reverse dependencies

Imports Me (28): Chromatograms, CompoundDb, DaparToolshed, hdxmsqc, MetaboAnnotation, MetaboCoreUtils, MetCirc, MsBackendMassbank, MsBackendMassIVE, MsBackendMetaboLights, MsBackendMetabolomicsWorkbench, MsBackendMgf, MsBackendMsp, MsBackendRawFileReader, MsBackendSql, MsFeatures, MSnbase, MsQuality, PSMatch, QFeatures, QFeaturesGUI, qmtools, scp, SmartPhos, Spectra, SpectraQL, SpectriPy, xcms

Suggests Me (3): MetNet, msqrob2, sfi