MSPrep

This package is for version 3.13 of Bioconductor; for the stable, up-to-date release version, see MSPrep.

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

Bioconductor version: 3.13

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>

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

Installation

To install this package, start R (version "4.1") 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")

Using MSPrep HTML R Script

Reference Manual PDF

NEWS Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews MassSpectrometry, Metabolomics, Preprocessing, Software

Version 1.2.0

In Bioconductor since BioC 3.12 (R-4.0) (3.5 years)

License GPL-3

Depends R (>= 4.0)

Imports SummarizedExperiment, S4Vectors, pcaMethods(>= 1.24.0), VIM, crmn, preprocessCore, sva, dplyr (>= 0.7), tidyr, tibble (>= 1.2), magrittr, rlang, stats, stringr, methods, ddpcr, missForest

System Requirements

URL https://github.com/KechrisLab/MSPrep

Bug Reports https://github.com/KechrisLab/MSPrep/issues

Suggests BiocStyle, knitr, rmarkdown, testthat (>= 1.0.2)

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