MSnbase
Base Functions and Classes for Mass Spectrometry and Proteomics
Bioconductor version: Release (3.19)
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")):
Installation
To install this package, start R (version "4.4") 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 | 2.30.1 |
| In Bioconductor since | BioC 2.8 (R-2.13) (13.5 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, 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, pryr, gridExtra, microbenchmark, zoo, knitr (>= 1.1.0), rols, Rdisop, pRoloc, pRolocdata(>= 1.7.1), msdata(>= 0.19.3), roxygen2, rgl, rpx, AnnotationHub, BiocStyle(>= 2.5.19), rmarkdown, imputeLCMD, norm, gplots, XML, shiny, magrittr, SummarizedExperiment |
| Linking To | Rcpp |
| Enhances | |
| Depends On Me | bandle, msmsEDA, msmsTests, pRolocGUI, pRoloc, qPLEXanalyzer, synapter, DAPARdata, pRolocdata, RforProteomics |
| Imports Me | CluMSID, DAPAR, DEP, MSnID, MSstatsQC, PrInCE, cliqueMS, peakPantheR, ptairMS, topdownr, xcms, qPLEXdata |
| Suggests Me | AnnotationHub, BiocGenerics, biobroom, isobar, msPurity, msqrob2, proDA, qcmetrics, wpm, msdata, enviGCMS, LCMSQA, pmd, RAMClustR |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | MSnbase_2.30.1.tar.gz |
| Windows Binary (x86_64) | MSnbase_2.30.1.zip (64-bit only) |
| macOS Binary (x86_64) | MSnbase_2.30.1.tgz |
| macOS Binary (arm64) | MSnbase_2.30.1.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 |