artMS
This is the development version of artMS; for the stable release version, see artMS.
Analytical R tools for Mass Spectrometry
Bioconductor version: Development (3.23)
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("artMS")):
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
BiocManager::install("artMS")
For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
| Reference Manual |
Details
| biocViews | Annotation, BiomedicalInformatics, Clustering, DifferentialExpression, GeneSetEnrichment, ImmunoOncology, MassSpectrometry, MultipleComparison, Normalization, Proteomics, QualityControl, Software, SystemsBiology |
| Version | 1.29.0 |
| In Bioconductor since | BioC 3.8 (R-3.5) (7 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
| 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
Follow Installation instructions to use this package in your R session.
| Source Package | |
| Windows Binary (x86_64) | |
| macOS Binary (x86_64) | |
| macOS Binary (arm64) | |
| Source Repository | git clone https://git.bioconductor.org/packages/artMS |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/artMS |
| Package Short Url | https://bioconductor.org/packages/artMS/ |
| Package Downloads Report | Download Stats |