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To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("gene2pathway")
In most cases, you don't need to download the package archive at all.
gene2pathway
|
This package is for version 2.8 of Bioconductor; for the stable, up-to-date release version, see gene2pathway.
Prediction of KEGG pathway membership for individual genes based on InterPro domain signatures
Bioconductor version: 2.8
The package takes a list of genes and predicts to which KEGG pathway each gene maps to. This is done by looking at the InterPro domains of each gene. Each prediction is assigned a confidence score. The package also allows to predict connected component membership of genes within signaling pathways. Separate models for each organism supported by KEGG can be trained.
Author: Holger Froehlich <frohlich at bit.uni-bonn.de>
Maintainer: Holger Froehlich <frohlich at bit.uni-bonn.de>
Citation (from within R,
enter citation("gene2pathway")):
Installation
To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("gene2pathway")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("gene2pathway")
| gene2pathway.pdf | ||
| Reference Manual |
Details
| biocViews | Bioinformatics, Classification, GraphsAndNetworks, Microarray, Pathways, Software |
| Version | 2.2.0 |
| In Bioconductor since | BioC 2.4 (R-2.9) (7 years) |
| License | GPL (>= 2) |
| Depends | R (>= 2.10.0), kernlab (>= 0.9), biomaRt(>= 1.12.1), KEGGSOAP(>= 1.12.0), RBGL, AnnotationDbi, org.Dm.eg.db, keggorthology(>= 2.0) |
| Imports | SSOAP, RCurl |
| LinkingTo | |
| Suggests | |
| SystemRequirements | |
| Enhances | doMC |
| URL | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | gene2pathway_2.2.0.tar.gz |
| Windows Binary | gene2pathway_2.2.0.zip |
| Mac OS X 10.6 (Snow Leopard) | |
| Mac OS X 10.9 (Mavericks) | |
| Subversion source | (username/password: readonly) |
| Git source | https://github.com/Bioconductor-mirror/gene2pathway/tree/release-2.8 |
| Package Short Url | http://bioconductor.org/packages/gene2pathway/ |
| Package Downloads Report | Download Stats |
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