MSnbase
This package is for version 3.14 of Bioconductor; for the stable, up-to-date release version, see MSnbase.
Base Functions and Classes for Mass Spectrometry and Proteomics
Bioconductor version: 3.14
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 and Lieven Clement.
Maintainer: Laurent Gatto <laurent.gatto at uclouvain.be>
citation("MSnbase")):
Installation
To install this package, start R (version "4.1") 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 | 2.20.4 |
| In Bioconductor since | BioC 2.8 (R-2.13) (13 years) |
| License | Artistic-2.0 |
| Depends | R (>= 3.5), methods, BiocGenerics(>= 0.7.1), Biobase(>= 2.15.2), mzR(>= 2.19.6), S4Vectors, ProtGenerics(>= 1.25.1) |
| Imports | MsCoreUtils, BiocParallel, IRanges(>= 2.13.28), plyr, vsn, grid, stats4, affy, impute, pcaMethods, MALDIquant (>= 1.16), mzID(>= 1.5.2), digest, lattice, ggplot2, XML, 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, shiny, magrittr, SummarizedExperiment |
| Linking To | Rcpp |
| Enhances | |
| Depends On Me | Autotuner, MetCirc, msmsEDA, msmsTests, pRoloc, pRolocdata, pRolocGUI, proteomics, qPLEXanalyzer, RforProteomics, synapter, xcms |
| Imports Me | cliqueMS, CluMSID, DAPAR, DAPARdata, DEP, MSnID, MSstatsQC, peakPantheR, POMA, PrInCE, ProteomicsAnnotationHubData, ptairMS, qPLEXdata, RMassBank, topdownr |
| Suggests Me | AnnotationHub, biobroom, BiocGenerics, isobar, msdata, msPurity, msqrob2, proDA, qcmetrics, wpm |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | MSnbase_2.20.4.tar.gz |
| Windows Binary | MSnbase_2.20.1.zip |
| macOS 10.13 (High Sierra) | MSnbase_2.20.0.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 3.14 | Source Archive |