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

Bioconductor version: Release (3.18)

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")):


To install this package, start R (version "4.3") and enter:

if (!require("BiocManager", quietly = TRUE))


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


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

Using MSPrep HTML R Script
Reference Manual PDF


biocViews MassSpectrometry, Metabolomics, Preprocessing, Software
Version 1.12.0
In Bioconductor since BioC 3.12 (R-4.0) (3.5 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
System Requirements
URL https://github.com/KechrisLab/MSPrep
Bug Reports https://github.com/KechrisLab/MSPrep/issues
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Suggests BiocStyle, knitr, rmarkdown, testthat (>= 1.0.2)
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Package Archives

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

Source Package MSPrep_1.12.0.tar.gz
Windows Binary MSPrep_1.12.0.zip (64-bit only)
macOS Binary (x86_64) MSPrep_1.12.0.tgz
macOS Binary (arm64)
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/
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