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 (3.21)
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:
Maintainer: Arnaud Wolfer <adwolfer at gmail.com>
citation("peakPantheR")):
Installation
To install this package, start R (version "4.5") 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 | ||
| NEWS | Text |
Details
| biocViews | MassSpectrometry, Metabolomics, PeakDetection, Software |
| Version | 1.21.0 |
| In Bioconductor since | BioC 3.10 (R-3.6) (5 years) |
| License | GPL-3 |
| Depends | R (>= 4.2) |
| 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 |
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_1.21.0.tar.gz |
| Windows Binary (x86_64) | peakPantheR_1.21.0.zip |
| macOS Binary (x86_64) | peakPantheR_1.21.0.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 |