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SteinerNet

R Package: Steiner tree approach for graph analysis

https://github.com/krashkov/steinernet

Science Score: 23.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ○
    CITATION.cff file
  • ○
    codemeta.json file
  • ○
    .zenodo.json file
  • ✓
    DOI references
    Found 2 DOI reference(s) in README
  • ○
    Academic publication links
  • ✓
    Committers with academic emails
    2 of 3 committers (66.7%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (12.5%) to scientific vocabulary

Keywords

biological-networks cran graph-algorithms r-language r-package steiner-heuristic steiner-tree steiner-tree-problem
Last synced: 6 months ago · JSON representation

Repository

R Package: Steiner tree approach for graph analysis

Basic Info
Statistics
  • Stars: 9
  • Watchers: 1
  • Forks: 4
  • Open Issues: 2
  • Releases: 3
Topics
biological-networks cran graph-algorithms r-language r-package steiner-heuristic steiner-tree steiner-tree-problem
Created over 7 years ago · Last pushed over 2 years ago
Metadata Files
Readme

README.md

SteinerNet

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 known to be NP-hard. 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.

Versions > 3.0.0

To get the latest version of the package and install it from CRAN run the following command:

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 < 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/

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.

Owner

  • Name: Aleksei Krasikov
  • Login: krashkov
  • Kind: user
  • Location: Frankfurt

C++ developer <3 math, algorithms and fast code

GitHub Events

Total
  • Watch event: 1
  • Issue comment event: 1
Last Year
  • Watch event: 1
  • Issue comment event: 1

Committers

Last synced: over 2 years ago

All Time
  • Total Commits: 44
  • Total Committers: 3
  • Avg Commits per committer: 14.667
  • Development Distribution Score (DDS): 0.114
Past Year
  • Commits: 0
  • Committers: 0
  • Avg Commits per committer: 0.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
Aleksei Krasikov k****s@p****u 39
Afshin Sadeghi s****n@g****m 3
Afshin Sadeghi s****i@i****e 2
Committer Domains (Top 20 + Academic)
informatik.uni-bonn.de: 1 phystech.edu: 1

Issues and Pull Requests

Last synced: about 2 years ago

All Time
  • Total issues: 4
  • Total pull requests: 1
  • Average time to close issues: 7 days
  • Average time to close pull requests: N/A
  • Total issue authors: 4
  • Total pull request authors: 1
  • Average comments per issue: 1.5
  • Average comments per pull request: 0.0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 2
  • Pull requests: 1
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Issue authors: 2
  • Pull request authors: 1
  • Average comments per issue: 0.5
  • Average comments per pull request: 0.0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • Anupriya014 (1)
  • YangLi-Bio (1)
  • krlmlr (1)
  • m-i-c-h-ael (1)
Pull Request Authors
  • elliotfontaine (2)
Top Labels
Issue Labels
help wanted (1) question (1) bug (1)
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • cran 326 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 1
  • Total versions: 8
  • Total maintainers: 1
cran.r-project.org: SteinerNet

Steiner Tree Approach for Graph Analysis

  • Versions: 8
  • Dependent Packages: 0
  • Dependent Repositories: 1
  • Downloads: 326 Last month
Rankings
Forks count: 10.8%
Stargazers count: 18.3%
Dependent repos count: 23.9%
Average: 26.4%
Dependent packages count: 28.7%
Downloads: 50.6%
Maintainers (1)
krasikov.as@phystech.edu
Last synced: 9 months ago