RforProteomics

Companion package to the 'Using R and Bioconductor for proteomics data analysis' publication

Bioconductor version: 3.23 · Package version: 1.50.0

This package contains code to illustrate the 'Using R and Bioconductor for proteomics data analysis' and 'Visualisation of proteomics data using R and Bioconductor' manuscripts. The vignettes describe the code and data needed to reproduce the examples and figures described in the paper and functionality for proteomics visualisation. It also contain various function to discover R software for mass spectrometry and proteomics.

Installation

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("RforProteomics")

Details

Maintainer	Laurent Gatto <laurent.gatto@uclouvain.be>
Author	Laurent Gatto [aut, cre], Sebastian Gibb [ctb], Vlad Petyuk [ctb], Thomas Pedersen Lin [ctb]
License	Artistic-2.0
URL	http://lgatto.github.com/RforProteomics/
Downloads rank	290
Source branch	RELEASE_3_23
biocViews	ExperimentData, MassSpectrometryData, ReproducibleResearch

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Source package

Dependencies

Depends: R (>= 3.5), MSnbase (>= 2.35.2)

Imports: R.utils, biocViews, BiocManager

Suggests: AnnotationDbi, rpx (>= 2.0.3), DT, knitr, rmarkdown, BiocStyle, mzR, xcms, msdata, MALDIquant (>= 1.12), MALDIquantForeign, readBrukerFlexData, Rdisop, OrgMassSpecR, SummarizedExperiment, BRAIN, rols, hpar, GO.db, org.Hs.eg.db, e1071, biomaRt, RColorBrewer, ggplot2, reshape2, xtable, lattice, mzID, pRoloc, pRolocdata, MSnID, msmsTests, msmsEDA, corrplot, beanplot, Heatplus, gplots, VennDiagram, protViz, genefilter, plotly, gridExtra, dplyr, lubridate, magick, cleaver

Reverse dependencies

Suggests Me (1): MSstatsQC