Steiner Tree Approach for Graph Analysis

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.

This R package was originally applied to analyzing biological networks. For more information about algorithms and their application, see original article and tutorial.

Installation

The installation process may differ to different versions of package. See information below.

Version 3.0.0

This is the current version of the package. It only requires installation of igraph package.

install.packages("SteinerNet")

Version 2.0

To install older versions of packages from CRAN, you need install_version() from devtools package. SteinerNet v2.0 works with igraph, limma and RBGL packages.

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")

Versions before 2.0

The installation process of older versions is similar to previous, but note, that they works with igraph0 package.

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")

Version history on Cran

https://cran.r-project.org/src/contrib/Archive/SteinerNet/

News

August 2018

SteinerNet v3.0.1 release.

  • If vertices of input graph of steinertree function has a name attribute, vertices of the output graph won't have realname attribute. The original names will be still at name attribute.

June 2018

SteinerNet v3.0.0 release. Main changes:

  • Critical bugs was fixed. A list may be provided on demand.
  • Structure of files and functions was refreshed
  • Backward incompatible changes were made (behavior of some functions and list of passed arguments was slightly changed). On the one hand, it makes the work with library simpler and more intuitive, but on the other hand, the workflow is changed too. So if you want to reproduce the results of the original article, please see tutorial and documentation.

November 2017

SteinerNet v2.0 release. Support of igraph graphs are added.

Citation

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.

News

Reference manual

It appears you don't have a PDF plugin for this browser. You can click here to download the reference manual.

install.packages("SteinerNet")

3.0.1 by Aleksei Krasikov, 9 months ago


https://github.com/krashkov/SteinerNet


Report a bug at https://github.com/krashkov/SteinerNet/issues


Browse source code at https://github.com/cran/SteinerNet


Authors: Afshin Sadeghi <[email protected]>


Documentation:   PDF Manual  


GPL-3 license


Imports grDevices, stats, utils, graphics

Depends on igraph

Suggests knitr, rmarkdown


See at CRAN