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artMS

Analytical R tools for Mass Spectrometry

Bioconductor version: Release (3.17)

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>

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

Installation

To install this package, start R (version "4.3") 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")
Learn to use artMS HTML R Script
Reference Manual PDF
NEWS Text
LICENSE Text

Details

biocViews Annotation, BiomedicalInformatics, Clustering, DifferentialExpression, GeneSetEnrichment, ImmunoOncology, MassSpectrometry, MultipleComparison, Normalization, Proteomics, QualityControl, Software, SystemsBiology
Version 1.18.0
In Bioconductor since BioC 3.8 (R-3.5) (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
Linking To
Suggests BiocStyle, ComplexHeatmap, factoextra, FactoMineR, gProfileR, knitr, PerformanceAnalytics, org.Mm.eg.db, rmarkdown, testthat
System Requirements
Enhances
URL http://artms.org
Bug Reports https://github.com/biodavidjm/artMS/issues
See More
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_1.18.0.tar.gz
Windows Binary artMS_1.18.0.zip
macOS Binary (x86_64) artMS_1.18.0.tgz
macOS Binary (arm64) artMS_1.18.0.tgz
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