This package is for version 3.15 of Bioconductor; for the stable, up-to-date release version, see RforProteomics.
Bioconductor version: 3.15
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.
Author: Laurent Gatto [aut, cre], Sebastian Gibb [ctb], Vlad Petyuk [ctb], Thomas Pedersen Lin [ctb]
Maintainer: Laurent Gatto <laurent.gatto at uclouvain.be>
Citation (from within R,
enter citation("RforProteomics")
):
To install this package, start R (version "4.2") and enter:
if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("RforProteomics")
For older versions of R, please refer to the appropriate Bioconductor release.
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("RforProteomics")
HTML | R Script | Using R for proteomics data analysis |
HTML | R Script | Visualisation of proteomics data using R and Bioconductor |
Reference Manual | ||
Text | NEWS |
biocViews | ExperimentData, MassSpectrometryData, ReproducibleResearch |
Version | 1.34.1 |
License | Artistic-2.0 |
Depends | R (>= 3.5), MSnbase(>= 2.5.3) |
Imports | R.utils, biocViews, BiocManager |
LinkingTo | |
Suggests | AnnotationDbi, rpx(>= 2.0.3), DT, knitr, rmarkdown, BiocStyle, mzR, xcms, msdata, isobar, 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, DEP, corrplot, beanplot, Heatplus, gplots, VennDiagram, protViz, genefilter, plotly, gridExtra, dplyr, lubridate, magick, cleaver |
SystemRequirements | |
Enhances | |
URL | http://lgatto.github.com/RforProteomics/ |
Depends On Me | |
Imports Me | |
Suggests Me | MSstatsQC |
Links To Me | |
Build Report |
Follow Installation instructions to use this package in your R session.
Source Package | RforProteomics_1.34.1.tar.gz |
Windows Binary | |
macOS Binary (x86_64) | |
Source Repository | git clone https://git.bioconductor.org/packages/RforProteomics |
Source Repository (Developer Access) | git clone [email protected]:packages/RforProteomics |
Package Short Url | https://bioconductor.org/packages/RforProteomics/ |
Package Downloads Report | Download Stats |
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