MSnbase

DOI:10.18129/B9.bioc.MSnbase

Base Functions and Classes for Mass Spectrometry and Proteomics

Bioconductor版本:版本(3.15)

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

Installation

To install this package, start R (version "4.2") and enter:

if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("MSnbase")

For older versions of R, please refer to the appropriateBioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("MSnbase")

HTML	R Script	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
PDF		Reference Manual

Details

biocViews	DataImport,ImmunoOncology,Infrastructure,MassSpectrometry,Proteomics,QualityControl,Software
Version	2.22.0
In Bioconductor since	BioC 2.8 (R-2.13) (11.5 years)
License	Artistic-2.0
Depends	R (>= 3.5), methods,BiocGenerics(>= 0.7.1),Biobase(>= 2.15.2),mzR(>= 2.29.3),S4Vectors,ProtGenerics(>= 1.27.2)
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
LinkingTo	Rcpp
Suggests	testthat,pryr,gridExtra,microbenchmark,zoo,knitr(>= 1.1.0),rols,Rdisop,pRoloc,pRolocdata(> = 1.7.1上),msdata(>= 0.19.3),roxygen2,rgl,rpx,AnnotationHub,BiocStyle(>= 2.5.19),rmarkdown,imputeLCMD,norm,gplots,shiny,magrittr,SummarizedExperiment
SystemRequirements
Enhances
URL	https://lgatto.github.io/MSnbase
BugReports	https://github.com/lgatto/MSnbase/issues
Depends On Me	Autotuner,bandle,DAPARdata,MetCirc,MobilityTransformR,msmsEDA,msmsTests,pRoloc,pRolocdata,pRolocGUI,proteomics,qPLEXanalyzer,RforProteomics,synapter,xcms
Imports Me	cliqueMS,CluMSID,DAPAR,DEP,MSnID,MSstatsQC,peakPantheR,PrInCE,ProteomicsAnnotationHubData,ptairMS,qPLEXdata,RMassBank,topdownr
Suggests Me	AnnotationHub,biobroom,BiocGenerics,isobar,msdata,msPurity,msqrob2,proDA,qcmetrics,wpm
Links To Me
Build Report

Package Archives

Follow2021年欧洲杯比分预测 instructions to use this package in your R session.

Source Package	MSnbase_2.22.0.tar.gz
Windows Binary	MSnbase_2.22.0.zip
macOS 10.13 (High Sierra)	MSnbase_2.22.0.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	//www.andersvercelli.com/packages/MSnbase/
Package Downloads Report	Download Stats