peakPantheR

DOI: 10.18129/B9.bioc.peakPantheR    

This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see peakPantheR.

Peak Picking and Annotation of High Resolution Experiments

Bioconductor version: 3.12

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>

Installation

To install this package, start R (version "4.0") and enter:

if (!requireNamespace("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")

 

HTML	R Script	Getting Started with the peakPantheR package
HTML	R Script	Parallel Annotation
HTML	R Script	peakPantheR Graphical User Interface
HTML	R Script	Real Time Annotation
PDF		Reference Manual
Text		NEWS

Details

biocViews	MassSpectrometry, Metabolomics, PeakDetection, Software
Version	1.4.0
In Bioconductor since	BioC 3.10 (R-3.6) (1.5 years)
License	GPL-3
Depends	R (>= 4.0)
Imports	foreach (>= 1.4.4), doParallel (>= 1.0.11), ggplot2 (>= 2.2.1), 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), shinythemes (>= 1.1.1), shinycssloaders (>= 1.0.0), DT (>= 0.15), utils
LinkingTo
Suggests	testthat, faahKO, msdata, knitr, rmarkdown, pander, BiocStyle
SystemRequirements
Enhances
URL	https://github.com/phenomecentre/peakPantheR
BugReports	https://github.com/phenomecentre/peakPantheR/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.

Source Package	peakPantheR_1.4.0.tar.gz
Windows Binary	peakPantheR_1.4.0.zip
macOS 10.13 (High Sierra)	peakPantheR_1.4.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/peakPantheR
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/peakPantheR
Package Short Url	https://bioconductor.org/packages/peakPantheR/
Package Downloads Report	Download Stats