mzID
This is the development version of mzID; for the stable release version, see mzID.
An mzIdentML parser for R
Bioconductor version: Development (3.24)
A parser for mzIdentML files implemented using the XML package. The parser tries to be general and able to handle all types of mzIdentML files with the drawback of having less 'pretty' output than a vendor specific parser. Please contact the maintainer with any problems and supply an mzIdentML file so the problems can be fixed quickly.
Author: Laurent Gatto [ctb, cre]
, Thomas Pedersen [aut]
, Vladislav Petyuk [ctb]
Maintainer: Laurent Gatto <laurent.gatto at uclouvain.be>
citation("mzID")):
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("mzID")
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("mzID")| Using mzID | R Script | |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | DataImport, ImmunoOncology, MassSpectrometry, Proteomics, Software |
| Version | 1.51.0 |
| In Bioconductor since | BioC 2.13 (R-3.0) (13 years) |
| License | GPL (>= 2) |
| Depends | methods |
| Imports | XML, plyr, parallel, doParallel, foreach, iterators, ProtGenerics |
| System Requirements | |
| URL |
See More
| Suggests | knitr, testthat |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | MSnbase, MSnID, TargetDecoy |
| Suggests Me | mzR, PSMatch, RforProteomics, PepMapViz |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | mzID_1.51.0.tar.gz |
| Windows Binary (x86_64) | mzID_1.51.0.zip (64-bit only) |
| macOS Binary (big-sur-x86_64) | mzID_1.51.0.tgz |
| macOS Binary (sonoma-arm64) | mzID_1.51.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/mzID |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/mzID |
| Bioc Package Browser | https://code.bioconductor.org/browse/mzID/ |
| Package Short Url | https://bioconductor.org/packages/mzID/ |
| Package Downloads Report | Download Stats |