artMS
This is the released version of artMS; for the devel version, see artMS.
All Bioconductor versions of artMS
3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9, 3.8
Analytical R tools for Mass Spectrometry
Bioconductor version: 3.23 · Package version: 1.29.0
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"):
David Jimenez-Morales, Alexandre Rosa Campos, John Von Dollen, Nevan Krogan, Danielle Swaney. artMS: Analytical R tools for Mass Spectrometry. doi:10.18129/B9.bioc.artMS, R package version 1.29.0, https://bioconductor.org/packages/artMS.
Generated from the package metadata; it may differ from the package's own citation.
Installation
To install this package, start R (version "4.6") 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.
Details
| Version | 1.29.0 |
| License | GPL (>= 3) + file LICENSE |
| URL | http://artms.org |
| Bug Reports | https://github.com/biodavidjm/artMS/issues |
| In Bioconductor since | BioC 3.8 (R-3.5) (7 years) |
| Downloads rank | 1406 of 2,418 |
| Source branch | RELEASE_3_23 |
| Build report | Bioconductor build system, r-universe |
| biocViews | Annotation, BiomedicalInformatics, Clustering, DifferentialExpression, GeneSetEnrichment, ImmunoOncology, MassSpectrometry, MultipleComparison, Normalization, Proteomics, QualityControl, Software, SystemsBiology |
| Package Short Url | https://bioconductor.org/packages/artMS/ |
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("artMS")| artMS: Analytical R Tools for Mass Spectrometry | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Download
Follow the installation instructions to use this package in your R session.
| Source package | artMS_1.29.0.tar.gz |
| Windows binary (x86_64) | artMS_1.29.0.zip |
| macOS binary (arm64) | artMS_1.29.0.tgz |
| macOS binary (x86_64) | artMS_1.29.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/artMS |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/artMS |
| Package Downloads Report | Download Stats |
Dependencies
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
Suggests: BiocStyle, ComplexHeatmap, factoextra, FactoMineR, gProfileR, knitr, PerformanceAnalytics, org.Mm.eg.db, rmarkdown, testthat