IPO
This package is for version 3.11 of Bioconductor; for the stable, up-to-date release version, see IPO.
Automated Optimization of XCMS Data Processing parameters
Bioconductor version: 3.11
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 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. 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("IPO")):
Installation
To install this package, start R (version "4.0") and enter:
if (!require("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")| XCMS Parameter Optimization with IPO | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | ImmunoOncology, MassSpectrometry, Metabolomics, Software |
| Version | 1.14.0 |
| In Bioconductor since | BioC 3.4 (R-3.3) (7.5 years) |
| License | GPL (>= 2) + file LICENSE |
| Depends | xcms(>= 1.50.0), rsm, CAMERA, grDevices, graphics, stats, utils |
| Imports | BiocParallel |
| System Requirements | |
| URL | https://github.com/rietho/IPO |
| Bug Reports | https://github.com/rietho/IPO/issues/new |
See More
| Suggests | RUnit, BiocGenerics, msdata, mtbls2, faahKO, knitr |
| Linking To | |
| Enhances | parallel |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | IPO_1.14.0.tar.gz |
| Windows Binary | IPO_1.14.0.zip |
| macOS 10.13 (High Sierra) | IPO_1.14.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/IPO |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/IPO |
| Bioc Package Browser | https://code.bioconductor.org/browse/IPO/ |
| Package Short Url | https://bioconductor.org/packages/IPO/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.11 | Source Archive |