MsCoreUtils
Core Utils for Mass Spectrometry Data
Bioconductor version: 3.24 · Package version: 1.25.4
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
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
| Maintainer | RforMassSpectrometry Package Maintainer <maintainer@rformassspectrometry.org> |
| Author | RforMassSpectrometry 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] |
| License | Artistic-2.0 |
| URL | https://github.com/RforMassSpectrometry/MsCoreUtils |
| Bug Reports | https://github.com/RforMassSpectrometry/MsCoreUtils/issues |
| Source branch | devel |
| Build report | Bioconductor build system, r-universe |
| biocViews | Infrastructure, MassSpectrometry, Metabolomics, Proteomics, Software |
| Package Short Url | https://bioconductor.org/packages/MsCoreUtils/ |
Citation
From within R, enter citation("MsCoreUtils"):
Laurent Gatto, Johannes Rainer, Sebastian Gibb, Philippine Louail, Adriano Rutz. MsCoreUtils: Core Utils for Mass Spectrometry Data. doi:10.18129/B9.bioc.MsCoreUtils, R package version 1.25.4, https://bioconductor.org/packages/MsCoreUtils.
Generated from the package metadata; it may differ from the package's own citation.
Documentation
Download
Follow the installation instructions to use this package in your R session.
| Source package | MsCoreUtils_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