peakPantheR

This is the released version of peakPantheR; for the devel version, see peakPantheR.

Peak Picking and Annotation of High Resolution Experiments

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DOI: 10.18129/B9.bioc.peakPantheR

Bioconductor version: Release (3.22)

An automated pipeline for the detection, integration and reporting of predefined features across a large number of mass spectrometry data files. It enables the real time annotation of multiple compounds in a single file, or the parallel annotation of multiple compounds in multiple files. A graphical user interface as well as command line functions will assist in assessing the quality of annotation and update fitting parameters until a satisfactory result is obtained.

Author: Arnaud Wolfer [aut, cre] ORCID iD ORCID: 0000-0001-5856-3218 , Goncalo Correia [aut] ORCID iD ORCID: 0000-0001-8271-9294 , Jake Pearce [ctb], Caroline Sands [ctb]

Maintainer: Arnaud Wolfer <adwolfer at gmail.com>

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

Installation

To install this package, start R (version "4.5") and enter:


if (!require("BiocManager", quietly = TRUE))
 install.packages("BiocManager")
BiocManager::install("peakPantheR")

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("peakPantheR")

Getting Started with the peakPantheR package HTML R Script

Parallel Annotation HTML R Script

peakPantheR Graphical User Interface HTML R Script

Real Time Annotation HTML R Script

Reference Manual PDF

NEWS Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews MassSpectrometry, Metabolomics, PeakDetection, Software

Version 1.24.0

In Bioconductor since BioC 3.10 (R-3.6) (6 years)

License GPL-3

Depends R (>= 4.5)

Imports foreach (>= 1.4.4), doParallel (>= 1.0.11), ggplot2 (>= 3.5.0), gridExtra (>= 2.3), MSnbase(>= 2.4.0), mzR(>= 2.12.0), stringr (>= 1.2.0), methods (>= 3.4.0), XML (>= 3.98.1.10), minpack.lm (>= 1.2.1), scales (>= 0.5.0), shiny (>= 1.0.5), bslib, shinycssloaders (>= 1.0.0), DT (>= 0.15), pracma (>= 2.2.3), utils, lubridate, svglite (>= 2.1.1)

System Requirements

URL https://github.com/phenomecentre/peakPantheR

Bug Reports https://github.com/phenomecentre/peakPantheR/issues/new

Suggests testthat, devtools, faahKO, msdata, knitr, rmarkdown, pander, BiocStyle

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