MSPrep

DOI: 10.18129/B9.bioc.MSPrep    

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

Bioconductor version: Release (3.12)

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 "4.0") and enter:

if (!requireNamespace("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 1.0.0
In Bioconductor since BioC 3.12 (R-4.0) (< 6 months)
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
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_1.0.0.tar.gz
Windows Binary MSPrep_1.0.0.zip
macOS 10.13 (High Sierra) MSPrep_1.0.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/MSPrep
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/MSPrep
Package Short Url https://bioconductor.org/packages/MSPrep/
Package Downloads Report Download Stats

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