artMS

This is the development version of artMS; for the stable release version, see artMS.

Analytical R tools for Mass Spectrometry

Bioconductor version: Development (3.21)

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] (ORCID: ), Alexandre Rosa Campos [aut, ctb] (ORCID: ), John Von Dollen [aut], Nevan Krogan [aut] (ORCID: ), Danielle Swaney [aut, ctb] (ORCID: )

Maintainer: David Jimenez-Morales <biodavidjm at gmail.com>

Citation (from within R, enter citation("artMS")):

Installation

To install this package, start R (version "4.5") 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 appropriate Bioconductor release.

Documentation

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

browseVignettes("artMS")

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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	Annotation, BiomedicalInformatics, Clustering, DifferentialExpression, GeneSetEnrichment, ImmunoOncology, MassSpectrometry, MultipleComparison, Normalization, Proteomics, QualityControl, Software, SystemsBiology
Version	1.25.0
In Bioconductor since	BioC 3.8 (R-3.5) (6 years)
License	GPL (>= 3) + file LICENSE
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
System Requirements
URL	http://artms.org
Bug Reports	https://github.com/biodavidjm/artMS/issues

Suggests	BiocStyle, ComplexHeatmap, factoextra, FactoMineR, gProfileR, knitr, PerformanceAnalytics, org.Mm.eg.db, rmarkdown, testthat
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report	Build Report

Package Archives

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

Source Package	artMS_1.25.0.tar.gz
Windows Binary (x86_64)
macOS Binary (x86_64)
macOS Binary (arm64)
Source Repository	git clone https://git.bioconductor.org/packages/artMS
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/artMS
Bioc Package Browser	https://code.bioconductor.org/browse/artMS/
Package Short Url	https://bioconductor.org/packages/artMS/
Package Downloads Report	Download Stats