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 (3.24)
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("peakPantheR")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
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 | 1.27.0 |
| In Bioconductor since | BioC 3.10 (R-3.6) (7 years) |
| License | GPL-3 |
| Depends | R (>= 4.5) |
| 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_1.27.0.tar.gz |
| Windows Binary (x86_64) | peakPantheR_1.27.0.zip |
| macOS Binary (big-sur-x86_64) | peakPantheR_1.27.0.tgz |
| macOS Binary (sonoma-arm64) | peakPantheR_1.27.0.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 |