artMS
This is thereleased version of artMS; for the devel version, seeartMS.
Analytical R tools for Mass Spectrometry
Bioconductor version: Release (3.22)
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("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 appropriateBioconductor 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 | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | Annotation,BiomedicalInformatics,Clustering,DifferentialExpression,GeneSetEnrichment,ImmunoOncology,MassSpectrometry,MultipleComparison,Normalization,Proteomics,QualityControl,Software,SystemsBiology |
| Version | 1.28.0 |
| In Bioconductor since | BioC 3.8 (R-3.5) (7 years) |
| License | GPL (>= 3) + fileLICENSE |
| 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
| 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
FollowInstallation instructions to use this package in your R session.
| Source Package | artMS_1.28.0.tar.gz |
| Windows Binary (x86_64) | artMS_1.28.0.zip |
| macOS Binary (x86_64) | artMS_1.28.0.tgz |
| macOS Binary (arm64) | artMS_1.28.0.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 |