Ipo R T E 2020

Ipo r t e 2020

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DOI: 10.18129/B9.bioc.IPO    

Automated Optimization of XCMS Data Processing parameters

Bioconductor version: Release (3.10)

The outcome of XCMS data processing strongly depends on the parameter settings.

IPO (`Isotopologue Parameter Optimization`) is a parameter optimization tool that is applicable for different kinds of samples and liquid chromatography coupled to high resolution mass spectrometry devices, fast and free of labeling steps.

Ipo r t e 2020

IPO uses natural, stable 13C isotopes to calculate a peak picking score. Retention time correction is optimized by minimizing the relative retention time differences within features and grouping parameters are optimized by maximizing the number of features showing exactly one peak from each injection of a pooled sample.

Ipo r t e 2020

The different parameter settings are achieved by design of experiment. The resulting scores are evaluated using response surface models.

Author: Gunnar Libiseller <Gunnar.Libiseller at joanneum.at>, Christoph Magnes <christoph.magnes at joanneum.at>, Thomas Riebenbauer <Thomas.Riebenbauer at joanneum.at>

Maintainer: Thomas Riebenbauer <Thomas.Riebenbauer at joanneum.at>

Citation (from within R, enter ):

Installation

To install this package, start R (version "3.6") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("IPO")

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("IPO")

 

HTMLR ScriptXCMS Parameter Optimization with IPO
PDF Reference Manual
Text NEWS
Text LICENSE

Details

biocViewsImmunoOncology, MassSpectrometry, Metabolomics, Software
Version1.12.0
In Bioconductor sinceBioC 3.4 (R-3.3) (3 years)
LicenseGPL (>= 2) + file LICENSE
Dependsxcms(>= 1.50.0), rsm, CAMERA, grDevices, graphics, stats, utils
ImportsBiocParallel
LinkingTo
SuggestsRUnit, BiocGenerics, msdata, mtbls2, faahKO, knitr
SystemRequirements
Enhancesparallel
URLhttps://github.com/rietho/IPO
BugReportshttps://github.com/rietho/IPO/issues/new
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.

Ipo r t e 2020