artMS

DOI: 10.18129/B9.bioc.artMS    

Analytical R tools for Mass Spectrometry

Bioconductor version: Release (3.8)

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.

Author: David Jimenez-Morales, Alexandre Rosa Campos, John Von Dollen.

Maintainer: David Jimenez-Morales <biodavidjm at gmail.com>

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

Installation

To install this package, start R (version "3.5") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("artMS", version = "3.8")

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")

 

HTML R Script Learn to use artMS ~30 min
PDF   Reference Manual
Text   NEWS
Text   LICENSE

Details

biocViews Annotation, BiomedicalInformatics, Clustering, DifferentialExpression, GeneSetEnrichment, MassSpectrometry, Normalization, Proteomics, QualityControl, Software, SystemsBiology
Version 1.0.1
License GPL (>= 3) + file LICENSE
Depends R (>= 3.5.0)
Imports AnnotationDbi, biomaRt, bit64, circlize, cluster, ComplexHeatmap, corrplot, data.table, dplyr, factoextra, FactoMineR, getopt, ggdendro, ggplot2, gplots, ggrepel, gProfileR, graphics, grDevices, grid, limma, MSstats, openxlsx, org.Hs.eg.db, org.Mm.eg.db, PerformanceAnalytics, pheatmap, plotly, plyr, RColorBrewer, reshape2, seqinr, stats, stringr, tidyr, UpSetR, utils, VennDiagram, yaml
LinkingTo
Suggests BiocStyle, knitr, rmarkdown, testthat
SystemRequirements
Enhances
URL https://github.com/biodavidjm/artMS
BugReports https://github.com/biodavidjm/artMS/issues
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_1.0.1.tar.gz
Windows Binary artMS_1.0.1.zip
Mac OS X 10.11 (El Capitan) artMS_1.0.1.tgz
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 http://bioconductor.org/packages/artMS/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.8 Source Archive

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