A set of functions for finding and analysing Steiner trees. It has applications in
biological pathway network analysis. Sadeghi (2013)
The Steiner tree problem on unweighted graphs seeks a minimum subtree (i.e. subtree with minimal number of edges), containing a given subset of the vertices (terminals). This problem is NP-complete. This package provides several heuristic and one exact approach for finding Steiner trees, as well as tools for analyzing resultant trees and comparing different algorithms.
The installation process may differ to different versions of package. See information below.
This is the current version of the package. It only requires installation of
To install older versions of packages from CRAN, you need
devtools package. SteinerNet v2.0 works with
install.packages("igraph") source("https://bioconductor.org/biocLite.R") biocLite("RBGL") source("https://bioconductor.org/biocLite.R") biocLite("limma") install_version("SteinerNet", version = "2.0")
The installation process of older versions is similar to previous, but note, that they works with
install_version("igraph0", version = "0.5.7") source("https://bioconductor.org/biocLite.R") biocLite("RBGL") source("https://bioconductor.org/biocLite.R") biocLite("limma") install_version("SteinerNet", version = "1.x")
SteinerNet v3.0.1 release.
steinertreefunction has a
nameattribute, vertices of the output graph won't have
realnameattribute. The original names will be still at
SteinerNet v3.0.0 release. Main changes:
SteinerNet v2.0 release. Support of igraph graphs are added.
To use this code in your research please cite this article related to this package:
Afshin Sadeghi and Holger Froehlich, "Steiner tree methods for optimal sub-network identification: an empirical study", BMC Bioinformatics 2013 14:144 doi:10.1186/1471-2105-14-144.