iDINGO 1.0.4 – Integrative Differential Network Analysis in Genomics

iDINGO 1.0.4

:: DESCRIPTION

iDINGO is an R package to estimate group-specific integrative networks and make inference on the integrative differential networks, considering the biological hierarchy among the platforms

::DEVELOPER

iDINGO team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / MacOsX
  • R

:: DOWNLOAD

 iDINGO

:: MORE INFORMATION

Citation:

Class CA, Ha MJ, Baladandayuthapani V, Do KA.
iDINGO-integrative differential network analysis in genomics with Shiny application.
Bioinformatics. 2018 Apr 1;34(7):1243-1245. doi: 10.1093/bioinformatics/btx750. PMID: 29194470; PMCID: PMC6030922.

DINGO: Differential Network Analysis in Genomics.
Ha MJ, Baladandayuthapani V, Do KA.
Bioinformatics. 2015 Jul 6. pii: btv406.

stringgaussnet 1.1 – PPI and Gaussian Network Construction from Transcriptomic Analysis Results Integrating a Multilevel Factor

stringgaussnet 1.1

:: DESCRIPTION

stringgaussnet is a toolbox for a construction of protein-protein interaction networks through the ‘STRING’ application programming interface, and an inference of Gaussian networks through ‘SIMoNe’ and ‘WGCNA’ approach, from DE genes analysis results and expression data. Additional functions are provided to import automatically networks into an active ‘Cytoscape’ session.

::DEVELOPER

Emmanuel Chaplais <emmanuel.chaplais at inserm.fr>, Henri-Jean Garchon

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux/ MacOsX
  • R

:: DOWNLOAD

 stringgaussnet

:: MORE INFORMATION

Citation

stringgaussnet: from differentially expressed genes to semantic and gaussian networks generation.
Chaplais E, Garchon HJ.
Bioinformatics. 2015 Jul 30. pii: btv450.

directPA 1.5 – Direction Pathway Analysis

directPA 1.5

:: DESCRIPTION

directPA is a package for pathway analysis in experiments with multiple perturbation designs.

::DEVELOPER

Pengyi Yang ,Ellis Patrick

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux /  Windows / MacOsX
  • R
:: DOWNLOAD

 directPA

:: MORE INFORMATION

Citation

Bioinformatics. 2014 Mar 15;30(6):808-14. doi: 10.1093/bioinformatics/btt616. Epub 2013 Oct 27.
Direction pathway analysis of large-scale proteomics data reveals novel features of the insulin action pathway.
Yang P1, Patrick E, Tan SX, Fazakerley DJ, Burchfield J, Gribben C, Prior MJ, James DE, Hwa Yang Y.

MoNetFamily – Homologous Modules and Module-module Interaction Networks in Vertebrates

MoNetFamily

:: DESCRIPTION

The MoNetFamily web server can identify the modules, homologous modules (called module family), and MMI networks across multiple species for the query protein(s).

::DEVELOPER

MoNetFamily team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2012 Jul;40(Web Server issue):W263-70. doi: 10.1093/nar/gks541. Epub 2012 Jun 11.
MoNetFamily: a web server to infer homologous modules and module-module interaction networks in vertebrates.
Lin CY1, Lin YW, Yu SW, Lo YS, Yang JM.

PanGIA 3.0 – Analysis of Physical and Genetic Interactions to infer Genetic Module Maps

PanGIA 3.0

:: DESCRIPTION

PanGIA (Physical and Genetic Interaction Alignment) is a plugin designed to integrate physical and genetic interactions into hierarchical module maps.

::DEVELOPER

PanGIA team

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • Java
  • Cytoscape
:: DOWNLOAD

 PanGIA

:: MORE INFORMATION

Citation

F1000Res. 2014 Jul 1;3:150. doi: 10.12688/f1000research.4546.1. eCollection 2014.
Porting and using PanGIA for Cytoscape 3: challenges and solutions.
Welker D, Demchak B

CyNeo4j 1.3 – A Cytoscape app to connect to a Neo4j database

CyNeo4j 1.3

:: DESCRIPTION

CyNeo4j allows users to connect to a Neo4j server to use the server as a storage for large graphs, a calculation platform through plugins in Neo4j or query the graph with Cypher.

::DEVELOPER

CyNeo4j team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • Java
  • Cytoscape
  • Neo4j
:: DOWNLOAD

 CyNeo4j

:: MORE INFORMATION

Citation

cyNeo4j: connecting Neo4j and Cytoscape.
Summer G, Kelder T, Ono K, Radonjic M, Heymans S, Demchak B.
Bioinformatics. 2015 Aug 12. pii: btv460.

Multi-netclust – Finding Connected Clusters in multi-parametric Networks

Multi-netclust

:: DESCRIPTION

Multi-netclust is an efficient tool to detect connected clusters in large biological networks represented by different data matrices.

::DEVELOPER

Wageningen University Bioinformatics group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX

:: DOWNLOAD

 Multi-netclust

:: MORE INFORMATION

Citation

Bioinformatics. 2010 Oct 1;26(19):2482-3. doi: 10.1093/bioinformatics/btq435. Epub 2010 Aug 2.
Multi-netclust: an efficient tool for finding connected clusters in multi-parametric networks.
Kuzniar A1, Dhir S, Nijveen H, Pongor S, Leunissen JA.

Omix 2.0.5 – Solutions for Systems Biology

Omix 2.0.5

:: DESCRIPTION

Omix is a user-friendly and highly customizable editor and modeling tool for metabolic network diagrams, equipped with extensive data visualization features. Main application fields are the interactive mapping of multi-omics data in the direct context of network drawings, in particular in the fields of transcriptomics, metabolomics and fluxomics.

::DEVELOPER

Omix® Visualization

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • Java

:: DOWNLOAD

 Omix

:: MORE INFORMATION

Citation

Visual Workflows for 13C-Metabolic Flux Analysis.
h K, Droste P, Wiechert W.
Bioinformatics. 2014 Oct 7. pii: btu585.

Droste, P., Miebach, S., Niedenführ, S., Wiechert, W., and h, K. 2011.
Visualizing multi-omics data in metabolic networks with the software Omix-A case study.
Biosystems, 105 (2), 154?161.

BiNoM 2.5 – Cytoscape plug-in for Manipulating and Analysing biological networks

BiNoM 2.5

:: DESCRIPTION

BiNoM (Biological Network Manager )is a Cytoscape plugin, developed to facilitate the manipulation of biological networks represented in standard systems biology formats (SBML, SBGN, BioPAX) and to carry out studies on the network structure. BiNoM provides the user with a complete interface for the analysis of biological networks in Cytoscape environment.

::DEVELOPER

Computational Systems Biology of Cancer group in Bioinformatics Laboratory of Institut Curie (Paris).

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

 BiNoM

:: MORE INFORMATION

Citation:

BiNoM 2.0, a Cytoscape plugin for accessing and analyzing pathways using standard systems biology formats.
Bonnet E, Calzone L, Rovera D, Stoll G, Barillot E, Zinovyev A.
BMC Syst Biol. 2013 Mar 1;7:18. doi: 10.1186/1752-0509-7-18.

Zinovyev A., Viara E., Calzone L., Barillot E.
BiNoM: a Cytoscape plugin for manipulating and analyzing biological networks. 2008.
Bioinformatics 24(6):876-877

DeDaL – Producing an Morphing data-driven and structure-driven Network Layouts

DeDaL

:: DESCRIPTION

DeDaL (Data-Driven network Layout) is a Cytoscape 3 app, which uses linear and non-linear algorithms of dimension reduction to produce data-driven network layouts based on multidimensional data (typically gene expression).

::DEVELOPER

Bioinformatics and Computational Systems Biology of Cancer

:: SCREENSHOTS

 

:: REQUIREMENTS

  • Linux/ Windows/ MacOsX
  • Java
  • Cytoscape

:: DOWNLOAD

 DeDaL

:: MORE INFORMATION

Citation

DeDaL: Cytoscape 3 app for producing and morphing data-driven and structure-driven network layouts.
Czerwinska U, Calzone L, Barillot E, Zinovyev A.
BMC Syst Biol. 2015 Aug 14;9:46. doi: 10.1186/s12918-015-0189-4.