MsBackendRawFileReader
This is the development version of MsBackendRawFileReader; for the stable release version, see MsBackendRawFileReader.
Mass Spectrometry Backend for Reading Thermo Fisher Scientific raw Files
Bioconductor version: Development (3.24)
implements a MsBackend for the Spectra package using Thermo Fisher Scientific's NewRawFileReader .Net libraries. The package is generalizing the functionality introduced by the rawrr package Methods defined in this package are supposed to extend the Spectra Bioconductor package.
Author: Christian Panse [aut, cre]
, Tobias Kockmann [aut]
, Roger Gine Bertomeu [ctb]
Maintainer: Christian Panse <cp at fgcz.ethz.ch>
citation("MsBackendRawFileReader")):
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("MsBackendRawFileReader")
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("MsBackendRawFileReader")| On Using and Extending the `MsBackendRawFileReader` Backend. | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| INSTALL | Text |
Details
| biocViews | MassSpectrometry, Metabolomics, Proteomics, Software |
| Version | 1.19.0 |
| In Bioconductor since | BioC 3.14 (R-4.1) (5 years) |
| License | GPL-3 |
| Depends | R (>= 4.1), methods, Spectra(>= 1.15.10) |
| Imports | ProtGenerics(>= 1.35.3), MsCoreUtils, S4Vectors, IRanges, rawrr(>= 1.17.2), utils, BiocParallel |
| System Requirements | mono-runtime 4.x or higher (including System.Data library) on Linux/macOS, .Net Framework (>= 4.5.1) on Microsoft Windows. |
| URL | https://github.com/fgcz/MsBackendRawFileReader |
| Bug Reports | https://github.com/fgcz/MsBackendRawFileReader/issues |
See More
| Suggests | BiocStyle(>= 2.5), ExperimentHub, MsBackendMgf, knitr, lattice, mzR, protViz (>= 0.7), rmarkdown, tartare(>= 1.5), 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 | MsBackendRawFileReader_1.19.0.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (big-sur-x86_64) | MsBackendRawFileReader_1.19.0.tgz |
| macOS Binary (sonoma-arm64) | MsBackendRawFileReader_1.19.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/MsBackendRawFileReader |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/MsBackendRawFileReader |
| Bioc Package Browser | https://code.bioconductor.org/browse/MsBackendRawFileReader/ |
| Package Short Url | https://bioconductor.org/packages/MsBackendRawFileReader/ |
| Package Downloads Report | Download Stats |