MSPrep

DOI: 10.18129/B9.bioc.MSPrep  

Package for Summarizing, Filtering, Imputing, and Normalizing Metabolomics Data

Bioconductor version: Release (3.16)

Package performs summarization of replicates, filtering by frequency, several different options for imputing missing data, and a variety of options for transforming, batch correcting, and normalizing data.

Author: Max McGrath [aut, cre], Matt Mulvahill [aut], Grant Hughes [aut], Sean Jacobson [aut], Harrison Pielke-lombardo [aut], Katerina Kechris [aut, cph, ths]

Maintainer: Max McGrath <max.mcgrath at ucdenver.edu>

Installation

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

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

BiocManager::install("MSPrep")

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("MSPrep")

 

HTML	R Script	Using MSPrep
PDF		Reference Manual
Text		NEWS

Details

biocViews	MassSpectrometry, Metabolomics, Preprocessing, Software
Version	1.8.0
In Bioconductor since	BioC 3.12 (R-4.0) (2.5 years)
License	GPL-3
Depends	R (>= 4.1.0)
Imports	SummarizedExperiment, S4Vectors, pcaMethods(>= 1.24.0), crmn, preprocessCore, dplyr (>= 0.7), tidyr, tibble (>= 1.2), magrittr, rlang, stats, stringr, methods, missForest, sva, VIM
LinkingTo
Suggests	BiocStyle, knitr, rmarkdown, testthat (>= 1.0.2)
SystemRequirements
Enhances
URL	https://github.com/KechrisLab/MSPrep
BugReports	https://github.com/KechrisLab/MSPrep/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	MSPrep_1.8.0.tar.gz
Windows Binary	MSPrep_1.8.0.zip
macOS Binary (x86_64)	MSPrep_1.8.0.tgz
macOS Binary (arm64)	MSPrep_1.8.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/MSPrep
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/MSPrep
Bioc Package Browser	https://code.bioconductor.org/browse/MSPrep/
Package Short Url	https://bioconductor.org/packages/MSPrep/
Package Downloads Report	Download Stats