NaviGO – An analytic tool for Gene Ontology Visualization and Similarity

NaviGO

:: DESCRIPTION

NaviGO is a web-based tool for interactive visualization, retrieval, and computation of functional similarity and associations of GO terms and genes.

::DEVELOPER

Kihara Bioinformatics Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

NaviGO: interactive tool for visualization and functional similarity and coherence analysis with gene ontology.
Wei Q, Khan IK, Ding Z, Yerneni S, Kihara D.
BMC Bioinformatics. 2017 Mar 20;18(1):177. doi: 10.1186/s12859-017-1600-5.

VRMLGen 1.4.6 – An R Package for 3D Data Visualization on the Web

VRMLGen 1.4.6

:: DESCRIPTION

VRMLGen is a free R software package to generate 3D representations of biological data in the Virtual Reality Markup Language

::DEVELOPER

VRMLGen team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux
  • R

:: DOWNLOAD

VRMLGen

:: MORE INFORMATION

Citation

Enrico Glaab, Jonathan M. Garibaldi, Natalio Krasnogor
vrmlgen: An R Package for 3D Data Visualization on the Web
Journal of Statistical Software, 2010 DOI: 10.18637/jss.v036.i08

CAVER 3.02 / CAVER Analyst 2.0 – software tool for Protein Analysis and Visualization

CAVER 3.02 / CAVER Analyst 2.0

:: DESCRIPTION

CAVER is a software tool for analysis and visualization of tunnels and channels in protein structures. Tunnels are void pathways leading from a cavity buried in a protein core to the surrounding solvent. Unlike tunnels, channels lead through the protein structure and their both endings are opened to the surrounding solvent. Studying of these pathways is highly important for drug design and molecular enzymology.

CAVER can be used either as PyMol plugin or independent application CAVER Analyst.

::DEVELOPER

Protein Engineering Group, Loschmidt Laboratories

:: SCREENSHOTS

CAVER

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • Java

:: DOWNLOAD

 CAVER / CAVER Analyst 

 :: MORE INFORMATION

Citation

Bioinformatics. 2014 May 29. pii: btu364. [Epub ahead of print]
CAVER Analyst 1.0: Graphic tool for interactive visualization and analysis of tunnels and channels in protein structures.
Kozlikova B, Sebestova E, Sustr V, Brezovsky J, Strnad O, Daniel L, Bednar D, Pavelka A, Manak M, Bezdeka M, Benes P, Kotry M, Gora A, Damborsky J, Sochor J.

CAVER 3.0: a tool for the analysis of transport pathways in dynamic protein structures.
Chovancova E, Pavelka A, Benes P, Strnad O, Brezovsky J, Kozlikova B, Gora A, Sustr V, Klvana M, Medek P, Biedermannova L, Sochor J, Damborsky J.
PLoS Comput Biol. 2012;8(10):e1002708. doi: 10.1371/journal.pcbi.1002708.

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

GIVE v0.2.0 – Genomic Interaction Visualization Engine

GIVE v0.2.0

:: DESCRIPTION

GIVE is an open source programming library that allows anyone without much programming experience to build custom genome browser websites or apps. With a few lines of codes, one can set up GIVE service on a local machine, manage custom data and build an interactive genome browser.

::DEVELOPER

Zhong Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows
  • Web Server

:: DOWNLOAD

GIVE

:: MORE INFORMATION

Citation

GIVE: portable genome browsers for personal websites.
Cao X, Yan Z, Wu Q, Zheng A, Zhong S.
Genome Biol. 2018 Jul 18;19(1):92. doi: 10.1186/s13059-018-1465-6.

EXPANDER 7.2 – Gene Expression Analysis & Visualization

EXPANDER 7.2

:: DESCRIPTION

EXPANDER (EXpression Analyzer and DisplayER) is a java-based tool for analysis of gene expression data.It is capable of (1) preprocessing (2) visualizing (3) clustering (4) biclustering and (5) performing downstream analysis of clusters and biclusters such as functional enrichment and promoter analysis It seamlessly integrates in one package all analysis steps, including:

  • Data preprocessing and normalization
  • Identification of differential genes
  • Clustering and biclustering;
  • Down-stream enrichment analyses of:
    – GO functional categories
    – TF binding sites in promoter regions
    – MicroRNA sites in 3′-UTRs and
    – Chromosomal locations
  • Network-based analysis of the expression data.

EXPANDER provides support for analysis of human, mouse, rat, chicken, fly, zebrafish, C. elegans, yeast (s.cerevisiaeand s. pombe), arabidopsis, tomato, listeria, A. fumigatus and E. coli.

::DEVELOPER

Ron Shamir’s lab

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

EXPANDER

:: MORE INFORMATION

Citation

Expander: from expression microarrays to networks and functions.
Ulitsky I, Maron-Katz A, Shavit S, Sagir D, Linhart C, Elkon R, Tanay A, Sharan R, Shiloh Y, Shamir R.
Nat Protoc. 2010 Feb;5(2):303-22. doi: 10.1038/nprot.2009.230.

Enrichment Map 3.2.1 – Cytoscape plugin for Functional Enrichment Visualization

Enrichment Map 3.2.1

:: DESCRIPTION

EnrichmentMap is a Cytoscape plugin for functional enrichment visualization. Enrichment results have to be generated outside Enrichment Map, using any of the available methods. Gene-sets, such as pathways and Gene Ontology terms, are organized into a network (i.e. the “enrichment map”). In this way, mutually overlapping gene-sets cluster together, making interpretation easier. Enrichment Map also enables the comparison of two different enrichment results in the same map.

::DEVELOPER

Bader Lab

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

 EnrichmentMap

:: MORE INFORMATION

Citation

Merico D, Isserlin R, Stueker O, Emili A, Bader GD
Enrichment Map: A Network-Based Method for Gene-Set Enrichment Visualization and Interpretation
PLoS One. 2010 Nov 15;5(11):e13984

Genonets 201805 – Analysis and Visualization of Genotype Networks

Genonets 201805

:: DESCRIPTION

Genonets Server is a tool that provides the following features: (i) the construction of genotype networks for categorical and univariate phenotypes from DNA, RNA, amino acid or binary sequences; (ii) analyses of genotype network topology and how it relates to robustness and evolvability, as well as analyses of genotype network topography and how it relates to the navigability of a genotype network via mutation and natural selection; (iii) multiple interactive visualizations that facilitate exploratory research and education.

::DEVELOPER

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Genonets server-a web server for the construction, analysis and visualization of genotype networks.
Khalid F, Aguilar-Rodríguez J, Wagner A, Payne JL.
Nucleic Acids Res. 2016 Apr 22. pii: gkw313.

VANTED 2.6.5 – Visualization and Analysis of Networks containing Experimental Data

VANTED 2.6.5

:: DESCRIPTION

VANTED (Visualisation and Analysis of Networks containing Experimental Data) is an open source software that offers the possibility to load and edit graphs, which may represent biological pathways or functional hierarchies. It allows to integrate different *omics data into the functional context and provides a variety of functions for data mapping and processing, statistical analysis, and visualisation. With the VANTED Add-on interface it is easily possible to extend the functionality of the software.

::DEVELOPER

Life Science Informatics – Prof. Dr. Falk Schreiber

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux/  MacOSX
  • Java

:: DOWNLOAD

 VANTED

:: MORE INFORMATION

Citation

Klukas and Schreiber (2010)
Integration of -omics data and networks for biomedical research with VANTED.
Journal of Integrative Biology, 7(2)

Björn H. Junker, Christian Klukas and Falk Schreiber (2006)
VANTED: A system for advanced data analysis and visualization in the context of biological networks.
BMC Bioinformatics, 7:109

expVIP 20180914 – RNA-seq Data Analysis and Visualization Platform

expVIP 20180914

:: DESCRIPTION

ExpVIP (expression visualization and integration platfor) is a tool that enables the integration of different RNA-Seq studies by analysing the data uniformly across experiments and provides a web interface to query the data.

::DEVELOPER

the Earlham Institute.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

expVIP

:: MORE INFORMATION

Citation

expVIP: a Customizable RNA-seq Data Analysis and Visualization Platform.
Borrill P, Ramirez-Gonzalez R, Uauy C.
Plant Physiol. 2016 Apr;170(4):2172-86. doi: 10.1104/pp.15.01667.