RforProteomics
This package is for version 3.7 of Bioconductor; for the stable, up-to-date release version, see RforProteomics.
Companion package to the 'Using R and Bioconductor for proteomics data analysis' publication
Bioconductor version: 3.7
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], Thomas Lin Pedersen [ctb], Sebastian Gibb [ctb], Vlad Petyuk [ctb]
Maintainer: Laurent Gatto <lg390 at cam.ac.uk>
citation("RforProteomics")):
Installation
To install this package, start R (version "3.5") 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.
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("RforProteomics")| Visualisation of proteomics data using R and Bioconductor | HTML | R Script |
| Visualisation of proteomics data using R and Bioconductor | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | ExperimentData, MassSpectrometryData, ReproducibleResearch |
| Version | 1.18.1 |
| License | Artistic-2.0 |
| Depends | MSnbase(>= 2.5.3) |
| Imports | R.utils, Biobase, rpx, biocViews, BiocInstaller, interactiveDisplay, DT, AnnotationDbi, shiny |
| System Requirements | |
| URL | http://lgatto.github.com/RforProteomics/ |
See More
| Suggests | knitr, rmarkdown, BiocStyle, mzR, xcms, msdata, isobar, MALDIquant (>= 1.12), MALDIquantForeign, readBrukerFlexData, rTANDEM, synapter, synapterdata, IPPD, Rdisop, OrgMassSpecR, SummarizedExperiment, BRAIN, rols, hpar, GO.db, org.Hs.eg.db, e1071, biomaRt, RColorBrewer, ggplot2, reshape2, xtable, lattice, mzID, pRoloc, pRolocdata, MSGFplus, MSGFgui, MSnID, msmsTests, msmsEDA, DEP, corrplot, beanplot, Heatplus, gplots, VennDiagram, protViz, genefilter |
| Linking To | |
| Enhances | cleaver |
| Depends On Me | |
| Imports Me | |
| Suggests Me | MSstatsQC, proteoQC, qcmetrics |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | RforProteomics_1.18.1.tar.gz |
| Windows Binary | |
| Mac OS X 10.11 (El Capitan) | |
| Source Repository | git clone https://git.bioconductor.org/packages/RforProteomics |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/RforProteomics |
| Package Short Url | https://bioconductor.org/packages/RforProteomics/ |
| Package Downloads Report | Download Stats |