MSnbase
Base Functions and Classes for Mass Spectrometry and Proteomics
Bioconductor version: 3.23 · Package version: 2.38.0
MSnbase provides infrastructure for manipulation, processing and visualisation of mass spectrometry and proteomics data, ranging from raw to quantitative and annotated data.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("MSnbase")Details
| Maintainer | Laurent Gatto <laurent.gatto@uclouvain.be> |
| 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. |
| License | Artistic-2.0 |
| URL | https://lgatto.github.io/MSnbase |
| Bug Reports | https://github.com/lgatto/MSnbase/issues |
| Downloads rank | 4493 |
| Source branch | RELEASE_3_23 |
| biocViews | DataImport, ImmunoOncology, Infrastructure, MassSpectrometry, Proteomics, QualityControl, Software |
Documentation
- A short introduction to MSnbase development
- MSnbase: MS data processing, visualisation and quantification
- MSnbase benchmarking
- MSnbase IO capabilities
- MSnbase: centroiding of profile-mode MS data
Download
Dependencies
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
LinkingTo: Rcpp
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
Reverse dependencies
Depends On Me (10): bandle, DAPARdata, MetaboAnnotatoR, msmsEDA, msmsTests, pRoloc, pRolocdata, pRolocGUI, qPLEXanalyzer, RforProteomics
Imports Me (18): Aerith, cliqueMS, CluMSID, DAPAR, lcmsPlot, MSnID, MSstatsQC, omXplore, peakPantheR, PrInCE, PRONE, ptairMS, qPLEXanalyzer, qPLEXdata, RMassBank, squallms, topdownr, xcms
Suggests Me (15): AnnotationHub, biobroom, BiocGenerics, faahKO, isobar, LCMSQA, msdata, msPurity, msqrob2, mtbls2, PepMapViz, proDA, qcmetrics, qPLEXanalyzer, wpm