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To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("STRINGdb")
In most cases, you don't need to download the package archive at all.
STRINGdb
STRINGdb (Search Tool for the Retrieval of Interacting proteins database)
Bioconductor version: 3.0
The STRINGdb package provides a user-friendly interface to the STRING protein-protein interactions database ( http://www.string-db.org ).
Author: Andrea Franceschini <andrea.franceschini at isb-sib.ch>
Maintainer: Andrea Franceschini <andrea.franceschini at isb-sib.ch>, Alexander Roth <alexander.roth at gmail.com>, Christian Von Mering <mering at imls.uzh.ch>, Michael Kuhn <michael.kuhn at biotec.tu-dresden.de>, Lars J Jensen <lars.juhl.jensen at gmail.com>
Citation (from within R,
enter citation("STRINGdb")):
Installation
To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("STRINGdb")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("STRINGdb")
| R Script | STRINGdb Vignette | |
| Reference Manual |
Details
| biocViews | Network, Software |
| Version | 1.5.5 |
| In Bioconductor since | BioC 2.13 (R-3.0) |
| License | GPL-2 |
| Depends | R (>= 2.14.0), png, sqldf, plyr, igraph, RCurl, plotrix, methods, RColorBrewer, gplots, hash |
| Imports | |
| LinkingTo | |
| Suggests | RUnit, BiocGenerics |
| SystemRequirements | |
| Enhances | |
| URL | |
| Depends On Me | scsR |
| Imports Me | |
| Suggests Me | |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | STRINGdb_1.5.5.tar.gz |
| Windows Binary | STRINGdb_1.5.5.zip |
| Mac OS X 10.6 (Snow Leopard) | STRINGdb_1.5.5.tgz |
| Mac OS X 10.9 (Mavericks) | STRINGdb_1.5.5.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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