peakPantheR

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see peakPantheR.

Peak Picking and Annotation of High Resolution Experiments


Bioconductor version: 3.16

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 "4.2") 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

Details

biocViews MassSpectrometry, Metabolomics, PeakDetection, Software
Version 1.12.2
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
See More
Suggests testthat, devtools, faahKO, msdata, knitr, rmarkdown, pander, BiocStyle
Linking To
Enhances
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 peakPantheR_1.12.2.tar.gz
Windows Binary peakPantheR_1.12.2.zip
macOS Binary (x86_64) peakPantheR_1.12.2.tgz
macOS Binary (arm64) peakPantheR_1.12.2.tgz
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
Old Source Packages for BioC 3.16 Source Archive