lcmsPlot
This is the released version of lcmsPlot; for the devel version, see lcmsPlot.
Comprehensive Liquid Chromatography-Mass Spectrometry (LC-MS) data visualisation package
Bioconductor version: Release (3.23)
lcmsPlot is an R package designed for visualising Liquid Chromatography-Mass Spectrometry (LC-MS) data with publication-ready high-quality plots. The package enables users to generate and customise chromatograms, mass traces, spectra, and more with fine-tuned aesthetics and annotation options.
Author: Ossama Edbali [aut, cre]
, Ralf Johannes Maria Weber [aut]
Maintainer: Ossama Edbali <o.edbali at bham.ac.uk>
citation("lcmsPlot")):
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")
BiocManager::install("lcmsPlot")
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("lcmsPlot")| Creating publication-ready LC-MS data plots | HTML | R Script |
| Easy-to-use, intuitive, and efficient LC-MS data plotting with lcmsPlot | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | MassSpectrometry, Metabolomics, Software |
| Version | 1.0.0 |
| In Bioconductor since | BioC 3.23 (R-4.6) (< 6 months) |
| License | GPL-3 |
| Depends | R (>= 4.4.0) |
| Imports | methods, rlang, dplyr, tibble, tidyr, BiocParallel, MSnbase, xcms, MsExperiment, mzR, Spectra, MsBackendMsp, S4Vectors, ggplot2, scales, patchwork, DBI, RSQLite |
| System Requirements | |
| URL | https://github.com/computational-metabolomics/lcmsPlot |
| Bug Reports | https://github.com/computational-metabolomics/lcmsPlot/issues |
See More
| Suggests | knitr, rmarkdown, BiocStyle, openxlsx, faahKO, rawrr, testthat (>= 3.0.0) |
| 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 | lcmsPlot_1.0.0.tar.gz |
| Windows Binary (x86_64) | lcmsPlot_1.0.0.zip |
| macOS Binary (big-sur-x86_64) | lcmsPlot_1.0.0.tgz |
| macOS Binary (sonoma-arm64) | lcmsPlot_1.0.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/lcmsPlot |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/lcmsPlot |
| Bioc Package Browser | https://code.bioconductor.org/browse/lcmsPlot/ |
| Package Short Url | https://bioconductor.org/packages/lcmsPlot/ |
| Package Downloads Report | Download Stats |