MsBackendMsp
This is the development version of MsBackendMsp; for the stable release version, see MsBackendMsp.
Mass Spectrometry Data Backend for NIST msp Files
Bioconductor version: Development (3.24)
Mass spectrometry (MS) data backend supporting import and handling of MS/MS spectra from NIST MSP Format (msp) files. Import of data from files with different MSP *flavours* is supported. Objects from this package add support for MSP files to Bioconductor's Spectra package. This package is thus not supposed to be used without the Spectra package that provides a complete infrastructure for MS data handling.
Author: Neumann Steffen [aut]
, Johannes Rainer [aut, cre]
, Michael Witting [ctb]
Maintainer: Johannes Rainer <Johannes.Rainer at eurac.edu>
citation("MsBackendMsp")):
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("MsBackendMsp")
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("MsBackendMsp")| MsBackendMsp | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | DataImport, Infrastructure, MassSpectrometry, Metabolomics, Proteomics, Software |
| Version | 1.17.0 |
| In Bioconductor since | BioC 3.15 (R-4.2) (4.5 years) |
| License | Artistic-2.0 |
| Depends | R (>= 4.1.0), Spectra(>= 1.5.14) |
| Imports | ProtGenerics(>= 1.35.3), BiocParallel, S4Vectors, IRanges, MsCoreUtils, methods, stats, data.table |
| System Requirements | |
| URL | https://github.com/RforMassSpectrometry/MsBackendMsp |
| Bug Reports | https://github.com/RforMassSpectrometry/MsBackendMsp/issues |
See More
| Suggests | testthat, knitr (>= 1.1.0), roxygen2, BiocStyle(>= 2.5.19), rmarkdown |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | lcmsPlot |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | MsBackendMsp_1.17.0.tar.gz |
| Windows Binary (x86_64) | MsBackendMsp_1.17.0.zip |
| macOS Binary (big-sur-x86_64) | MsBackendMsp_1.17.0.tgz |
| macOS Binary (sonoma-arm64) | MsBackendMsp_1.17.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/MsBackendMsp |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/MsBackendMsp |
| Bioc Package Browser | https://code.bioconductor.org/browse/MsBackendMsp/ |
| Package Short Url | https://bioconductor.org/packages/MsBackendMsp/ |
| Package Downloads Report | Download Stats |