DOI: 10.18129/B9.bioc.artMS    

This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see artMS.

Analytical R tools for Mass Spectrometry

Bioconductor version: 3.9

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 []( for details.

Author: David Jimenez-Morales, Alexandre Rosa Campos, John Von Dollen.

Maintainer: David Jimenez-Morales <biodavidjm at>

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


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biocViews Annotation, BiomedicalInformatics, Clustering, DifferentialExpression, GeneSetEnrichment, ImmunoOncology, MassSpectrometry, MultipleComparison, Normalization, Proteomics, QualityControl, Software, SystemsBiology
Version 1.2.7
In Bioconductor since BioC 3.8 (R-3.5) (1 year)
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,,, PerformanceAnalytics, pheatmap, plotly, plyr, RColorBrewer, scales, seqinr, stats, stringr, tidyr, UpSetR, utils, VennDiagram, yaml
Suggests BiocStyle, knitr, rmarkdown, testthat
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