MSnbase
This package is for version 3.6 of Bioconductor; for the stable, up-to-date release version, see MSnbase.
Base Functions and Classes for Mass Spectrometry and Proteomics
Bioconductor version: 3.6
MSnbase provides infrastructure to manipulation, processing and visualisation 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 and Martina Fisher.
Maintainer: Laurent Gatto <lg390 at cam.ac.uk>
citation("MSnbase")):
Installation
To install this package, start R (version "3.4") 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
| Reference Manual | |
| NEWS | Text |
Details
| biocViews | DataImport, Infrastructure, MassSpectrometry, Proteomics, QualityControl, Software |
| Version | 2.4.2 |
| In Bioconductor since | BioC 2.8 (R-2.13) (13 years) |
| License | Artistic-2.0 |
| Depends | R (>= 3.1), methods, BiocGenerics(>= 0.7.1), Biobase(>= 2.15.2), mzR(>= 2.11.11), BiocParallel, ProtGenerics(>= 1.9.1) |
| Imports | plyr, IRanges, preprocessCore, vsn, grid, stats4, affy, impute, pcaMethods, MALDIquant (>= 1.16), mzID(>= 1.5.2), digest, lattice, ggplot2, S4Vectors, XML, Rcpp |
| System Requirements | |
| URL | https://github.com/lgatto/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(>= 0.12.2), roxygen2, rgl, rpx, AnnotationHub, BiocStyle(>= 2.5.19), rmarkdown, imputeLCMD, norm, gplots, shiny |
| Linking To | Rcpp |
| Enhances | |
| Depends On Me | msmsEDA, msmsTests, ProCoNA, pRoloc, pRolocdata, pRolocGUI, proteoQC, RforProteomics, synapter, xcms |
| Imports Me | DAPAR, DAPARdata, DEP, MSnID, MSstats, MSstatsQC, Pbase, ProteomicsAnnotationHubData, RMassBank, topdownr |
| Suggests Me | AnnotationHub, biobroom, BiocGenerics, isobar, qcmetrics, readat, rpx |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | MSnbase_2.4.2.tar.gz |
| Windows Binary | MSnbase_2.4.2.zip (32- & 64-bit) |
| Mac OS X 10.11 (El Capitan) | MSnbase_2.4.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/MSnbase |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/MSnbase |
| Package Short Url | https://bioconductor.org/packages/MSnbase/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.6 | Source Archive |