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Bioconductor - artMS

artMS

This is the released version of artMS; for the devel version, see artMS.

Analytical R tools for Mass Spectrometry

Bioconductor version: Release (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: 0000-0003-4356-6461 , Alexandre Rosa Campos [aut, ctb] ORCID: 0000-0003-3988-7764 , John Von Dollen [aut], Nevan Krogan [aut] ORCID: 0000-0003-4902-337X , Danielle Swaney [aut, ctb] ORCID: 0000-0001-6119-6084

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")

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")
Details biocViews Annotation, BiomedicalInformatics, Clustering, DifferentialExpression, GeneSetEnrichment, ImmunoOncology, MassSpectrometry, MultipleComparison, Normalization, Proteomics, QualityControl, Software, SystemsBiology Version 1.26.0 In Bioconductor since BioC 3.8 (R-3.5) (6.5 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 See More Package Archives

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

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