MSnbase
This is the released version of MSnbase; for the devel version, see MSnbase.
Base Functions and Classes for Mass Spectrometry and Proteomics
Bioconductor version: Release (3.23)
MSnbase provides infrastructure for manipulation, processing and visualisation of mass spectrometry and proteomics data, ranging from raw to quantitative and annotated data.
Author: Laurent Gatto, Johannes Rainer and Sebastian Gibb with contributions from Guangchuang Yu, Samuel Wieczorek, Vasile-Cosmin Lazar, Vladislav Petyuk, Thomas Naake, Richie Cotton, Arne Smits, Martina Fisher, Ludger Goeminne, Adriaan Sticker, Lieven Clement and Pascal Maas.
Maintainer: Laurent Gatto <laurent.gatto at uclouvain.be>
citation("MSnbase")):
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("MSnbase")
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("MSnbase")| A short introduction to `MSnbase` development | HTML | R Script |
| Base Functions and Classes for MS-based Proteomics | HTML | R Script |
| MSnbase benchmarking | HTML | R Script |
| MSnbase IO capabilities | HTML | R Script |
| MSnbase: centroiding of profile-mode MS data | HTML | R Script |
| Reference Manual |
Details
| biocViews | DataImport, ImmunoOncology, Infrastructure, MassSpectrometry, Proteomics, QualityControl, Software |
| Version | 2.38.1 |
| In Bioconductor since | BioC 2.8 (R-2.13) (15.5 years) |
| License | Artistic-2.0 |
| Depends | R (>= 3.5), methods, BiocGenerics(>= 0.7.1), Biobase(>= 2.15.2), mzR(>= 2.29.3), S4Vectors, ProtGenerics(>= 1.29.1) |
| Imports | MsCoreUtils, PSMatch(>= 1.15.3), PTMods(>= 0.99.5), BiocParallel, IRanges(>= 2.13.28), plyr, vsn, grid, stats4, affy, impute, pcaMethods, MALDIquant (>= 1.16), mzID(>= 1.5.2), digest, lattice, ggplot2, scales, MASS, Rcpp |
| System Requirements | |
| URL | https://lgatto.github.io/MSnbase |
| Bug Reports | https://github.com/lgatto/MSnbase/issues |
See More
| Suggests | testthat, gridExtra, microbenchmark, zoo, knitr (>= 1.1.0), Rdisop, pRoloc, pRolocdata(>= 1.43.3), magick, MsDataHub, msdata, roxygen2, rgl, rpx, AnnotationHub, BiocStyle(>= 2.5.19), rmarkdown, imputeLCMD, norm, gplots, XML, shiny, magrittr, SummarizedExperiment, Spectra |
| Linking To | Rcpp |
| Enhances | |
| Depends On Me | bandle, MetaboAnnotatoR, msmsEDA, msmsTests, pRoloc, pRolocGUI, qPLEXanalyzer, DAPARdata, pRolocdata, RforProteomics |
| Imports Me | Aerith, cliqueMS, CluMSID, DAPAR, lcmsPlot, MSnID, MSstatsQC, omXplore, peakPantheR, PrInCE, PRONE, ptairMS, qPLEXanalyzer, RMassBank, squallms, topdownr, xcms, qPLEXdata |
| Suggests Me | AnnotationHub, biobroom, BiocGenerics, isobar, msPurity, msqrob2, proDA, qcmetrics, qPLEXanalyzer, wpm, faahKO, msdata, mtbls2, LCMSQA, PepMapViz |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | MSnbase_2.38.1.tar.gz |
| Windows Binary (x86_64) | MSnbase_2.38.0.zip |
| macOS Binary (big-sur-x86_64) | MSnbase_2.37.0.tgz |
| macOS Binary (sonoma-arm64) | MSnbase_2.38.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/MSnbase |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/MSnbase |
| Bioc Package Browser | https://code.bioconductor.org/browse/MSnbase/ |
| Package Short Url | https://bioconductor.org/packages/MSnbase/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.23 | Source Archive |