BANFF 2.0 – Gene Network Feature Selection

BANFF 2.0

:: DESCRIPTION

BANFF (Bayesian Network Feature Finder) is an R package for gene network feature selection.

::DEVELOPER

Tianwei Yu

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • R

:: DOWNLOAD

BANFF

:: MORE INFORMATION

Citation

Bayesian network feature finder (BANFF): an R package for gene network feature selection.
Lan Z, Zhao Y, Kang J, Yu T.
Bioinformatics. 2016 Dec 1;32(23):3685-3687.

JiffyNet – Jiffy (instant) Gene Network Modeler for newly Sequenced Species

JiffyNet

:: DESCRIPTION

JiffyNet specifically designed to instantly construct genome-scale protein networks based on associalogs (functional associations transferred from a template network by orthology) for a query species with only protein sequences provided.

::DEVELOPER

Network Biomedicine Laboratory at Yonsei University, Korea

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Eiru Kim, Hanhae Kim, Insuk Lee.
JiffyNet: a web-based instant protein network modeler for newly sequenced species,
Nucl. Acids Res. (1 July 2013) 41 (W1): W192-W197

GeneNetVal – Gene Network Biological Validity based on Gene-gene Interaction Relevance

GeneNetVal

:: DESCRIPTION

GeneNetVal is a Java application for network analysis. The application uses the metabolic pathways stored in kegg to rate the validity of an input network.

::DEVELOPER

GeneNetVal team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Windows
  • Java

:: DOWNLOAD

 GeneNetVal

:: MORE INFORMATION

Citation:

ScientificWorldJournal. 2014;2014:540679. doi: 10.1155/2014/540679. Epub 2014 Sep 8.
Gene network biological validity based on gene-gene interaction relevance.
Gómez-Vela F, Díaz-Díaz N.

GNC 1.3 – Gene Network Coherence with direct and indirect Relationships

GNC 1.3

:: DESCRIPTION

GNC is a Java-based software tool for analyzing gene networks coherence using direct and indirect relationships.

::DEVELOPER

GNC team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Windows
  • Java

:: DOWNLOAD

 GNC

:: MORE INFORMATION

Citation:

Gene network coherence based on prior knowledge using direct and indirect relationships.
Gómez-Vela F, Lagares JA, Díaz-Díaz N.
Comput Biol Chem. 2015 Jun;56:142-51. doi: 10.1016/j.compbiolchem.2015.03.002.

GeneNet 1.2.13 – Modeling and Inferring Gene Networks

GeneNet 1.2.13

:: DESCRIPTION

GeneNet is a package for analyzing gene expression (time series) data with focus on the inference of gene networks.

::DEVELOPER

Strimmer Lab

:: SCREENSHOTS

GeneNet

:: REQUIREMENTS

  • Windows / Linux / MacOSX
  • R package

:: DOWNLOAD

 GeneNet

:: MORE INFORMATION

Citation

BMC Syst Biol. 2007 Aug 6;1:37.
From correlation to causation networks: a simple approximate learning algorithm and its application to high-dimensional plant gene expression data.
Opgen-Rhein R, Strimmer K.

GFD-Net 1.2 – Measuring Semantic Dissimilarity of Gene Networks

GFD-Net 1.2

:: DESCRIPTION

GFD-Net is a Cytoscape app designed to visualize and analyze the functional dissimilarity of gene networks. GFD-Net can analyze a gene network based on Gene Ontology (GO) and calculate a quantitative measure of its functional dissimilarity, i.e. a quantitative value of the degree of dissimilarity between the connected genes in it.

::DEVELOPER

GFD-Net team

:: SCREENSHOTS

GFD-Net

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • Java
  • Cytoscape

:: DOWNLOAD

 GFD-Net

:: MORE INFORMATION

Citation

F1000Res. 2014 Jul 1;3:142. doi: 10.12688/f1000research.4573.1. eCollection 2014.
Development and use of the Cytoscape app GFD-Net for measuring semantic dissimilarity of gene networks.
Diaz-Montana JJ, Diaz-Diaz N

Red – Inference of Epistatic Gene Networks

Red

:: DESCRIPTION

Red is a conceptually new probabilistic approach to gene network inference from quantitative interaction data

::DEVELOPER

BioLab , University of Ljubljana

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

 Red

:: MORE INFORMATION

Citation

Bioinformatics. 2014 Jun 15;30(12):i246-i254. doi: 10.1093/bioinformatics/btu287.
Gene network inference by probabilistic scoring of relationships from a factorized model of interactions.
Zitnik M1, Župan B2.

FuseNet – Gene Network Inference by Fusing data from Diverse Distributions

FuseNet

:: DESCRIPTION

FuseNet is a Markov network formulation that infers networks from a collection of nonidentically distributed datasets.

::DEVELOPER

FuseNet team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

 FuseNet

:: MORE INFORMATION

Citation

Gene network inference by fusing data from diverse distributions.
Žitnik M, Zupan B.
Bioinformatics. 2015 Jun 15;31(12):i230-i239. doi: 10.1093/bioinformatics/btv258.

BUS 1.24.0 – Gene Network Reconstruction

BUS 1.24.0

:: DESCRIPTION

BUS can be used to compute associations among genes (gene-networks) or between genes and some external traits (i.e. clinical).

::DEVELOPER

Group of Clinical Genomic Networks

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / MacOsX
  • R package
  • BioConductor

:: DOWNLOAD

 BUS

:: MORE INFORMATION

SiGN-SSM 1.2.1 / SiGN-L1 1.0.0 – Gene Network Estimation Software

SiGN-SSM 1.2.1 / SiGN-L1 1.0.0

:: DESCRIPTION

SiGN-SSM  is open source gene network estimation software able to run in parallel on PCs and massively parallel supercomputers. The software estimates a state space model (SSM), that is a statistical dynamic model suitable for analyzing short time and/or replicated time series gene expression profiles. SiGN-SSM implements a novel parameter constraint effective to stabilize the estimated models. Also, by using a supercomputer, it is able to determine the gene network structure by the statistical permutation test in a practical time. SiGN-SSM is applicable not only to analyzing temporal regulatory dependencies between genes, but also to extracting the differentially regulated genes from time series expression profiles.

SiGN-L1 is network estimation software using sparse learning. It uses L1-regularization for simultaneous parameter estimation and model selection of statistical graphical models such as graphical Gaussian models and vector autoregressive models.

::DEVELOPER

SiGN-SSM TEam

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / Mac OsX

:: DOWNLOAD

 SiGN-SSM , SiGN-L1

:: MORE INFORMATION

Citation

Tamada, Y., Yamaguchi, R., Imoto, S., Hirose, O., Yoshida, R., Nagasaki, M., and Miyano, S. (2011).
SiGN-SSM: open source parallel software for estimating gene networks with state space models.
Bioinformatics. 2011 Apr 15;27(8):1172-3. doi: 10.1093/bioinformatics/btr078.

Genome Inform. 2011;25(1):40-52.
Sign: large-scale gene network estimation environment for high performance computing.
Tamada Y, Shimamura T, Yamaguchi R, Imoto S, Nagasaki M, Miyano S.