artMS

DOI:10.18129/B9.bioc.artMS

This is thedevelopmentversion of artMS; for the stable release version, seeartMS.

Analytical R tools for Mass Spectrometry

Bioconductor version: Development (3.16)

artMS provides a set of tools for the analysis of proteomics label-free datasets. It takes as input the MaxQuant search result output (evidence.txt file) and performs quality control, relative quantification using MSstats, downstream analysis and integration. artMS also provides a set of functions to re-format and make it compatible with other analytical tools, including, SAINTq, SAINTexpress, Phosfate, and PHOTON. Check [http://artms.org](http://artms.org) for details.

Author: David Jimenez-Morales [aut, cre], Alexandre Rosa Campos [aut, ctb], John Von Dollen [aut], Nevan Krogan [aut], Danielle Swaney [aut, ctb]

Maintainer: David Jimenez-Morales

Installation

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

if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager") # The following initializes usage of Bioc devel BiocManager::install(version='devel') BiocManager::install("artMS")

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

Documentation

查看文档的版本包age installed in your system, start R and enter:

browseVignettes("artMS")

HTML	R Script	Learn to use artMS
PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

biocViews	Annotation,BiomedicalInformatics,Clustering,DifferentialExpression,GeneSetEnrichment,ImmunoOncology,MassSpectrometry,MultipleComparison,Normalization,Proteomics,QualityControl,Software,SystemsBiology
Version	1.15.0
In Bioconductor since	BioC 3.8 (R-3.5) (3.5 years)
License	GPL (>= 3) + fileLICENSE
Depends	R (>= 4.1.0)
Imports	AnnotationDbi,bit64,circlize,cluster,corrplot,data.table,dplyr,getopt,ggdendro,ggplot2,gplots,ggrepel, graphics, grDevices, grid,limma,MSstats,openxlsx,org.Hs.eg.db,pheatmap,plotly,plyr,RColorBrewer,scales,seqinr, stats,stringr,tidyr,UpSetR, utils,VennDiagram,yaml
LinkingTo
Suggests	BiocStyle,ComplexHeatmap,factoextra,FactoMineR,gProfileR,knitr,PerformanceAnalytics,org.Mm.eg.db,rmarkdown,testthat
SystemRequirements
Enhances
URL	http://artms.org
BugReports	https://github.com/biodavidjm/artMS/issues
Depends On Me
Imports Me
Suggests Me
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	artMS_1.15.0.tar.gz
Windows Binary	artMS_1.15.0.zip
macOS 10.13 (High Sierra)	artMS_1.15.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/artMS
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/artMS
Package Short Url	//www.andersvercelli.com/packages/artMS/
Package Downloads Report	Download Stats