MsCoreUtils

DOI: 10.18129/B9.bioc.MsCoreUtils    

Core Utils for Mass Spectrometry Data

Bioconductor version: Release (3.15)

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), quantitative aggregation functions (median polish, robust summarisation, ...), missing data imputation, data normalisation (quantiles, vsn, ...) as well as misc helper functions, that are used across high-level data structure within the R for Mass Spectrometry packages.

Author: RforMassSpectrometry Package Maintainer [cre], Laurent Gatto [aut] , Johannes Rainer [aut] , Sebastian Gibb [aut] , Adriaan Sticker [ctb], Sigurdur Smarason [ctb], Thomas Naake [ctb], Josep Maria Badia Aparicio [ctb] , Michael Witting [ctb] , Samuel Wieczorek [ctb]

Maintainer: RforMassSpectrometry Package Maintainer <maintainer at rformassspectrometry.org>

Citation (from within R, enter citation("MsCoreUtils")):

Installation

To install this package, start R (version "4.2") and enter:

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

BiocManager::install("MsCoreUtils")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("MsCoreUtils")

 

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Details

biocViews Infrastructure, MassSpectrometry, Metabolomics, Proteomics, Software
Version 1.8.0
In Bioconductor since BioC 3.11 (R-4.0) (2.5 years)
License Artistic-2.0
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
SystemRequirements
Enhances
URL https://github.com/RforMassSpectrometry/MsCoreUtils
BugReports https://github.com/RforMassSpectrometry/MsCoreUtils/issues
Depends On Me
Imports Me CompoundDb, MetaboAnnotation, MetaboCoreUtils, MsBackendMassbank, MsBackendMgf, MsBackendMsp, MsBackendRawFileReader, MsFeatures, MSnbase, PSMatch, QFeatures, qmtools, scp, Spectra, xcms
Suggests Me MetNet, msqrob2
Links To Me
Build Report  

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package MsCoreUtils_1.8.0.tar.gz
Windows Binary MsCoreUtils_1.8.0.zip
macOS Binary (x86_64) MsCoreUtils_1.8.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/MsCoreUtils
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/MsCoreUtils
Package Short Url https://bioconductor.org/packages/MsCoreUtils/
Package Downloads Report Download Stats

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