Cytoscape 3.7.2 – Platform for Complex-Network Analysis & Visualization

Cytoscape 3.7.2

:: DESCRIPTION

Cytoscape is an open source bioinformatics software platform for visualizing molecular interaction networks and biological pathways and integrating these networks with annotations, gene expression profiles and other state data.

Although Cytoscape was originally designed for biological research, now it is a general platform for complex network analysis and visualization.

::DEVELOPER

Cytoscape Team

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux / Mac OsX
  • Java

:: DOWNLOAD

Cytoscape

:: MORE INFORMATION

Citation:

Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, Amin N, Schwikowski B, Ideker T.
Cytoscape: a software environment for integrated models of biomolecular interaction networks.
Genome Research 2003 Nov; 13(11):2498-504

HTSanalyzeR 2.22.0 – Network analysis of High Throughput Screens

HTSanalyzeR 2.22.0

:: DESCRIPTION

HTSanalyzeR provides classes and methods for gene set over-representation, enrichment and network analyses on high-throughput screens.

::DEVELOPER

the Markowetz lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX / Windows
  • R
  • BioCOnductor

:: DOWNLOAD

 HTSanalyzeR

:: MORE INFORMATION

Citation

Bioinformatics. 2011 Mar 15;27(6):879-80. doi: 10.1093/bioinformatics/btr028. Epub 2011 Jan 22.
HTSanalyzeR: an R/Bioconductor package for integrated network analysis of high-throughput screens.
Wang X1, Terfve C, Rose JC, Markowetz F.

PINBPA 1.1.8 – Cytoscape app for Network Analysis of GWAS data

PINBPA 1.1.8

:: DESCRIPTION

PINBPA (Protein interaction network-based pathway analysis) for genome-wide association studies (GWAS) has been developed as a Cytoscape app, to enable analysis of GWAS data in a network fashion.

::DEVELOPER

PINBPA team

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Linux/Windows/MacOsX
  • Java
  • Cytoscape

:: DOWNLOAD

 PINBPA

:: MORE INFORMATION

Citation

PINBPA: Cytoscape app for network analysis of GWAS data.
Wang L, Matsushita T, Madireddy L, Mousavi P, Baranzini S.
Bioinformatics. 2014 Sep 25. pii: btu644

DINGO 1.0 – Differential Network Analysis in Genomics

DINGO 1.0

:: DESCRIPTION

DINGO is a pathway-based differential network analysis in genomics model for estimating group-specific networks as well as making inference on the differential networks.

::DEVELOPER

Min Jin Ha <mjha@mdanderson.org>, Veerabhadran Baladandayuthapani , Kim-Anh Do

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / MacOsX
  • R

:: DOWNLOAD

 DINGO

:: MORE INFORMATION

Citation:

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

GenePEN – Network Analysis of Omics Data

GenePEN

:: DESCRIPTION

GenePEN, an efficient machine learning approach to identify coordinated alterations of genes or proteins in biological networks using omics data, providing provably optimal results in few seconds

::DEVELOPER

Bioinformatics Core, Luxembourg Centre for Systems Biomedicine (LCSB)

:: SCREENSHOTS

N/a

:: REQUIREMENTS

  • Windows/ Linux
  • MatLab

:: DOWNLOAD

 GenePEN

:: MORE INFORMATION

Citation

Stat Appl Genet Mol Biol. 2015 Feb 3. pii: /j/sagmb.ahead-of-print/sagmb-2014-0045/sagmb-2014-0045.xml. doi: 10.1515/sagmb-2014-0045. [Epub ahead of print]
GenePEN: analysis of network activity alterations in complex diseases via the pairwise elastic net.
Vlassis N, Glaab E.

SNPrank 0.1.0 – Network Analysis tool for GWAS

SNPrank 0.1.0

:: DESCRIPTION

SNPrank is an eigenvector centrality algorithm that ranks the importance of single nucleotide polymorphisms (SNPs) in a genetic association interaction network (GAIN). Each SNP is ranked according to its overall contribution to the phenotype, including its main effect and second- and higher-order gene-gene interactions.

::DEVELOPER

Insilico Research Group (McKinney Laboratory for Bioinformatics and In Silico Modeling)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • Python / Java / MatLab

:: DOWNLOAD

 pysnprank ,  matsnprank , jsnprank

:: MORE INFORMATION

Citation

Bioinformatics. 2011 Jan 15;27(2):284-5. doi: 10.1093/bioinformatics/btq638. Epub 2010 Nov 25.
Real-world comparison of CPU and GPU implementations of SNPrank: a network analysis tool for GWAS.
Davis NA, Pandey A, McKinney BA.

NeAT – Network Analysis Tools

NeAT

:: DESCRIPTION

NeAT is a toolbox for the analysis of biological networks, clusters, classes and pathways.

::DEVELOPER

NeAT Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 NeAT

:: MORE INFORMATION

Citation

Network Analysis Tools: from biological networks to clusters and pathways.
Brohée S, Faust K, Lima-Mendez G, Vanderstocken G, van Helden J.
Nat Protoc. 2008;3(10):1616-29. doi: 10.1038/nprot.2008.100.

NAIL 1.01 – Network Analysis in the Life Sciences

NAIL 1.01

:: DESCRIPTION

The NAIL (Network Analysis and Inference Library) project is a set of tools for solving problems in the life sciences using network (graph) approaches. NAIL includes methods for creating networks, analysing and comparing networks, and for visualising or presenting the results.

::DEVELOPER

NAIL team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux
  • MaxLab

:: DOWNLOAD

  NAIL

:: MORE INFORMATION

Citation

NAIL, a software toolset for inferring, analyzing and visualizing regulatory networks.
Hurley DG, Cursons J, Wang YK, Budden DM, Print CG, Crampin EJ.
Bioinformatics. 2014 Sep 21. pii: btu612.

NetComm 1.0 – A Network Analysis Tool Based on Communicability for Complex Biological Networks

NetComm 1.0

:: DESCRIPTION

NetComm is an R package for use in both human protein-protein interaction network analyses as well as analyses of arbitrary networks

::DEVELOPER

Shaw Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / Mac OsX
  • R

:: DOWNLOAD

 NetComm

:: MORE INFORMATION

Citation

NetComm: A Network Analysis Tool Based on Communicability for Complex Biological Networks.
Campbell IM, James RA, Chen ES, Shaw CA.
Bioinformatics. 2014 Aug 13. pii: btu536.

GenCLiP 2.0 – Human Gene Function And Network Analysis

GenCLiP 2.0

:: DESCRIPTION

GenCLiP is a literature mining tool that can cluster a list of genes with keywords that are auto-extracted from their up-to-date related literature and then manually curated by the user. GenCLiP can also generate a group of negative control genes and a group of positive control genes for comparing the cluster results with the analyzed genes to filter out un-specific keywords.

::DEVELOPER

ZHongxi Huang, Lab of Bioinformatics Cancer Institute ,  Southern Medical University

:: SCREENSHOTS

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Bioinformatics. 2014 Apr 23. pii: btu241. [Epub ahead of print]
GenCLiP 2.0: a web server for functional clustering of genes and construction of molecular networks based on free terms.
Wang JH, Zhao LF, Lin P, Su XR, Chen SJ, Huang LQ, Wang HF, Zhang H, Hu ZF, Yao KT, Huang ZX.

BMC Bioinformatics. 2008 Jul 13;9:308.
GenCLiP: a software program for clustering gene lists by literature profiling and constructing gene co-occurrence networks related to custom keywords.
Huang ZX, Tian HY, Hu ZF, Zhou YB, Zhao J, Yao KT.