rawDiag
This is the released version of rawDiag; for the devel version, see rawDiag.
Brings Orbitrap Mass Spectrometry Data to Life; Fast and Colorful
Bioconductor version: Release (3.23)
Optimizing methods for liquid chromatography coupled to mass spectrometry (LC-MS) poses a nontrivial challenge. The rawDiag package facilitates rational method optimization by generating MS operator-tailored diagnostic plots of scan-level metadata. The package is designed for use on the R shell or as a Shiny application on the Orbitrap instrument PC.
Author: Christian Panse [aut, cre]
, Christian Trachsel [aut], Tobias Kockmann [aut]
Maintainer: Christian Panse <cp at fgcz.ethz.ch>
citation("rawDiag")):
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("rawDiag")
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("rawDiag")| Brings Orbitrap Mass Spectrometry Data to Life; Fast and Colorful | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| INSTALL | Text |
Details
| biocViews | Infrastructure, MassSpectrometry, Metabolomics, Proteomics, ShinyApps, Software |
| Version | 1.8.0 |
| In Bioconductor since | BioC 3.19 (R-4.4) (2.5 years) |
| License | GPL-3 |
| Depends | R (>= 4.4) |
| Imports | dplyr, ggplot2 (>= 3.4), grDevices, hexbin, htmltools, BiocManager, BiocParallel, rawrr(>= 1.15.5), rlang, reshape2, scales, shiny (>= 1.5), stats, utils |
| System Requirements | |
| URL | https://github.com/fgcz/rawDiag/ |
| Bug Reports | https://github.com/fgcz/rawDiag/issues |
See More
| Suggests | BiocStyle(>= 2.28), ExperimentHub, tartare, knitr, testthat |
| 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 | rawDiag_1.8.0.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (big-sur-x86_64) | rawDiag_1.8.0.tgz |
| macOS Binary (sonoma-arm64) | rawDiag_1.8.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/rawDiag |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/rawDiag |
| Bioc Package Browser | https://code.bioconductor.org/browse/rawDiag/ |
| Package Short Url | https://bioconductor.org/packages/rawDiag/ |
| Package Downloads Report | Download Stats |