MsCoreUtils

DOI: 10.18129/B9.bioc.MsCoreUtils  

Core Utils for Mass Spectrometry Data

Bioconductor version: Release (3.16)

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>

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")

 

HTML	R Script	Core Utils for Mass Spectrometry Data
PDF		Reference Manual
Text		NEWS

Details

biocViews	Infrastructure, MassSpectrometry, Metabolomics, Proteomics, Software
Version	1.10.0
In Bioconductor since	BioC 3.11 (R-4.0) (3 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, missForest
SystemRequirements
Enhances	HDF5Array
URL	https://github.com/RforMassSpectrometry/MsCoreUtils
BugReports	https://github.com/RforMassSpectrometry/MsCoreUtils/issues
Depends On Me
Imports Me	CompoundDb, MetaboAnnotation, MetaboCoreUtils, MetCirc, 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_1.10.0.tar.gz
Windows Binary	MsCoreUtils_1.10.0.zip
macOS Binary (x86_64)	MsCoreUtils_1.10.0.tgz
macOS Binary (arm64)	MsCoreUtils_1.10.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/MsCoreUtils
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/MsCoreUtils
Bioc Package Browser	https://code.bioconductor.org/browse/MsCoreUtils/
Package Short Url	https://bioconductor.org/packages/MsCoreUtils/
Package Downloads Report	Download Stats