MsCoreUtils

This is the development version of MsCoreUtils; for the stable release version, see MsCoreUtils.

Core Utils for Mass Spectrometry Data

Bioconductor version: Development (3.21)

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.

Author: RforMassSpectrometry Package Maintainer [cre], Laurent Gatto [aut] (ORCID: ), Johannes Rainer [aut] (ORCID: ), Sebastian Gibb [aut] (ORCID: ), Philippine Louail [aut] (ORCID: ), Adriaan Sticker [ctb], Sigurdur Smarason [ctb], Thomas Naake [ctb], Josep Maria Badia Aparicio [ctb] (ORCID: ), Michael Witting [ctb] (ORCID: ), Samuel Wieczorek [ctb], Roger Gine Bertomeu [ctb] (ORCID: ), Mar Garcia-Aloy [ctb] (ORCID: )

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

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

Installation

To install this package, start R (version "4.5") and enter:


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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")

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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	Infrastructure, MassSpectrometry, Metabolomics, Proteomics, Software
Version	1.19.0
In Bioconductor since	BioC 3.11 (R-4.0) (4.5 years)
License	Artistic-2.0
Depends	R (>= 3.6.0)
Imports	methods, S4Vectors, MASS, stats, clue
System Requirements
URL	https://github.com/RforMassSpectrometry/MsCoreUtils
Bug Reports	https://github.com/RforMassSpectrometry/MsCoreUtils/issues

Suggests	testthat, knitr, BiocStyle, rmarkdown, roxygen2, imputeLCMD, impute, norm, pcaMethods, vsn, Matrix, preprocessCore, missForest
Linking To	Rcpp
Enhances	HDF5Array
Depends On Me
Imports Me	CompoundDb, hdxmsqc, MetaboAnnotation, MetaboCoreUtils, MetCirc, MsBackendMassbank, MsBackendMgf, MsBackendMsp, MsBackendRawFileReader, MsBackendSql, MsFeatures, MSnbase, PSMatch, QFeatures, qmtools, scp, Spectra, SpectraQL, xcms
Suggests Me	MetNet, msqrob2
Links To Me
Build Report	Build Report

Package Archives

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

Source Package	MsCoreUtils_1.19.0.tar.gz
Windows Binary (x86_64)	MsCoreUtils_1.19.0.zip
macOS Binary (x86_64)	MsCoreUtils_1.19.0.tgz
macOS Binary (arm64)	MsCoreUtils_1.19.0.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