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To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("RforProteomics")
In most cases, you don't need to download the package archive at all.
RforProteomics
Companion package to the 'Using R and Bioconductor for proteomics data analysis' publication
Bioconductor version: 3.0
This package contains code to illustrate the 'Using R and Bioconductor for proteomics data analysis' paper. Two vignettes describe the code and data needed to reproduce the examples and figures descibed in the paper and functionality for proteomics visualisation.
Author: Laurent Gatto [aut, cre], Thomas Lin Pedersen [ctb], Sebastian Gibb [ctb], Vlad Petyuk [ctb]
Maintainer: Laurent Gatto <lg390 at cam.ac.uk>
Citation (from within R,
enter citation("RforProteomics")):
Installation
To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("RforProteomics")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("RforProteomics")
| R Script | A current perspective on using R and Bioconductor for proteomics data analysis | |
| R Script | RforProteomics Bioc2013 poster | |
| R Script | Using R for proteomics data analysis | |
| HTML | R Script | Visualisation of proteomics data using R and Bioconductor |
| Reference Manual | ||
| Text | NEWS |
Details
| biocViews | ExperimentData, MassSpectrometry, MassSpectrometryData, Proteomics |
| Version | 1.4.1 |
| License | Artistic-2.0 |
| Depends | MSnbase |
| Imports | R.utils, Biobase, rpx, biocViews, BiocInstaller, interactiveDisplay, shiny |
| LinkingTo | |
| Suggests | mzR, xcms, msdata, isobar, MALDIquant (>= 1.11), MALDIquantForeign, readBrukerFlexData, rTANDEM, synapter, synapterdata, IPPD, Rdisop, OrgMassSpecR, BRAIN, rols, hpar, GO.db, org.Hs.eg.db, biomaRt, RColorBrewer, ggplot2, reshape2, xtable, lattice, mzID, pRoloc, pRolocdata, knitr, BiocStyle, MSGFplus, MSGFgui, MSnID |
| SystemRequirements | |
| Enhances | cleaver |
| URL | http://lgatto.github.com/RforProteomics/ |
| Depends On Me | |
| Imports Me | |
| Suggests Me | proteoQC, qcmetrics |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | RforProteomics_1.4.1.tar.gz |
| Windows Binary | RforProteomics_1.4.1.zip |
| Mac OS X 10.6 (Snow Leopard) | RforProteomics_1.4.1.tgz |
| Mac OS X 10.9 (Mavericks) | RforProteomics_1.4.1.tgz |
| Browse/checkout source | (username/password: readonly) |
| Package Downloads Report | Download Stats |
Common Bioconductor workflows include:
- Oligonucleotide Arrays
- High-throughput Sequencing
- Counting Reads for Differential Expression (parathyroideSE vignette)
- Annotation
- Annotating Variants
- Annotating Ranges
- Flow Cytometry and other assays
- Candidate Binding Sites for Known Transcription Factors
- Cloud-enabled cis-eQTL search and annotation
- RNA-Seq workflow: gene-level exploratory analysis and differential expression
- Changing genomic coordinate systems with rtracklayer::liftOver
- Mass spectrometry and proteomics data analysis
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