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This is the development version of peakPantheR; for the stable release version, see peakPantheR.

Peak Picking and Annotation of High Resolution Experiments

Bioconductor version: Development (3.19)

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] , Goncalo Correia [aut] , Jake Pearce [ctb], Caroline Sands [ctb]

Maintainer: Arnaud Wolfer <adwolfer at gmail.com>

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


To install this package, start R (version "4.4") and enter:

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

# The following initializes usage of Bioc devel


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:

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


biocViews MassSpectrometry, Metabolomics, PeakDetection, Software
Version 1.17.0
In Bioconductor since BioC 3.10 (R-3.6) (4.5 years)
License GPL-3
Depends R (>= 4.2)
Imports foreach (>= 1.4.4), doParallel (>= 1.0.11), ggplot2 (>= 3.3.0), gridExtra (>= 2.3), MSnbase(>= 2.4.0), mzR(>= 2.12.0), stringr (>= 1.2.0), methods (>= 3.4.0), XML (>=, 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
System Requirements
URL https://github.com/phenomecentre/peakPantheR
Bug Reports https://github.com/phenomecentre/peakPantheR/issues/new
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Suggests testthat, devtools, faahKO, msdata, knitr, rmarkdown, pander, BiocStyle
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Package Archives

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

Source Package peakPantheR_1.17.0.tar.gz
Windows Binary peakPantheR_1.17.0.zip (64-bit only)
macOS Binary (x86_64) peakPantheR_1.17.0.tgz
macOS Binary (arm64)
Source Repository git clone https://git.bioconductor.org/packages/peakPantheR
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/peakPantheR
Bioc Package Browser https://code.bioconductor.org/browse/peakPantheR/
Package Short Url https://bioconductor.org/packages/peakPantheR/
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