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peakPantheR

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")):

Installation

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


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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

Details

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 (>= 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
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/
Package Downloads Report Download Stats