artMS

DOI: 10.18129/B9.bioc.artMS    

This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see artMS.

Analytical R tools for Mass Spectrometry

Bioconductor version: 3.12

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 <biodavidjm at gmail.com>

Installation

To install this package, start R (version "4.0") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("artMS")

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("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	1.8.3
In Bioconductor since	BioC 3.8 (R-3.5) (2.5 years)
License	GPL (>= 3) + file LICENSE
Depends	R (>= 3.6.0)
Imports	AnnotationDbi, biomaRt, bit64, circlize, cluster, ComplexHeatmap, corrplot, data.table, dplyr, factoextra, FactoMineR, getopt, ggdendro, ggplot2, gplots, ggrepel, gProfileR, graphics, grDevices, grid, limma, MSstats, openxlsx, org.Hs.eg.db, org.Mm.eg.db, PerformanceAnalytics, pheatmap, plotly, plyr, RColorBrewer, scales, seqinr, stats, stringr, tidyr, UpSetR, utils, VennDiagram, yaml
LinkingTo
Suggests	BiocStyle, knitr, 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

Follow Installation instructions to use this package in your R session.

Source Package	artMS_1.8.3.tar.gz
Windows Binary	artMS_1.8.3.zip
macOS 10.13 (High Sierra)	artMS_1.8.3.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	https://bioconductor.org/packages/artMS/
Package Downloads Report	Download Stats