Tag: Visual Analysis

OrthoNets 1.0 – Simultaneous Visual Analysis of Orthologs and their Interaction Neighborhoods across different organisms

OrthoNets 1.0

:: DESCRIPTION

OrthoNets provides various information about the proteins and interactions – including domain architectures (bottom of figure 1), protein and gene aliases, pubmed identifiers of the publications supporting the interactions, and the experiment type used to detect the interaction. Here the view is focused on the RNA polymerase enzyme LEO1 – so that only the LEO1 node and its recorded interaction partners are displayed.

::DEVELOPER

The Wodak Lab

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

 OrthoNets

:: MORE INFORMATION

Citation

Yanqi Hao, Anna Merkovitch, James Vlasblom, Shuye Pu, Andrei L. Turinsky, Denitza Roudeva, Brian Turner, Jack Greenblatt, Shoshana J. Wodak.
OrthoNets: simultaneous visual analysis of orthologs and their interaction neighborhoods across different organisms.
Bioinformatics. 2011 Mar 15;27(6):883-4. Epub 2011 Jan 20.

PedVizApi 0.15 – Visual Analysis of large and complex Pedigrees

PedVizApi 0.15

:: DESCRIPTION

PedVizApi is a Java Api for the visual analysis of large and complex pedigrees. It provides all the necessary functionality for the interactive exploration of extended genealogies. Available packages are mostly focused on a static representation or cannot be added to an existing application; the goal of this open-source library is to provide an application program interface that enables the efficient construction of visual analytic applications for the analysis of family based data.

::DEVELOPER

the Center of Biomedicine (CBM) at EURAC research.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/windows/MacOsX
  • Java

:: DOWNLOAD

 PedVizApi

:: MORE INFORMATION

Citation

Fuchsberger, Falchi, Forer, Pramstaller (2007),
“PedVizApi: A Java API for the interactive, visual analysis of extended pedigrees“,
Bioinformatics, 24(2):279-281

AutoSNPa 20121128 – Visual analysis of SNP data for autozygosity Mapping

AutoSNPa 20121128

:: DESCRIPTION

AutoSNPa aids the identification of regions of Identity By Descent (IBD) in inbred families, by visually presenting colour-coded SNP genotype data ordered by physical or genetic distance.

::DEVELOPER

Ian’s DNA@Leeds

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows
  • Microsoft .NET framework version 2.0

:: DOWNLOAD

 AutoSNPa

:: MORE INFORMATION

Citation

Hum Mutat. 2006 Oct;27(10):1041-6.
Interactive visual analysis of SNP data for rapid autozygosity mapping in consanguineous families.
Carr IM, Flintoff KJ, Taylor GR, Markham AF, Bonthron DT.

RenoDoI 1.1.0 – Visual Analysis of Biological Data-knowledge Networks

RenoDoI 1.1.0

:: DESCRIPTION

RenoDoI is a visual analytics approach to untangle (lt. renodare) large and dense integrated data-knowledge networks using degree-of-interest (DoI) functions with attribute-based layouts of the resulting subnetworks.

:: DEVELOPER

RenoDoI team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • Java
  • Cytoscape

:: DOWNLOAD

 RenoDoI

:: MORE INFORMATION

Citation

Visual analysis of biological data-knowledge networks
Vehlow C, Kao DP, Bristow MR, Hunter LE, Weiskopf D, Görg C.
BMC Bioinformatics. 2015 Apr 29;16(1):135.

BicOverlapper 2.0 – Visual Analysis of Gene Expression

BicOverlapper 2.0

:: DESCRIPTION

BicOverlapper is a framework to support visual analysis of gene expression by means of biclustering.

BicOverlapper is a tool to visualize biclusters from gene-expression matrices in a way that helps to compare biclustering methods, to unravel trends and to highlight relevant genes and conditions. A visual approach can complement biological and statistical analysis and reduce the time spent by specialists interpreting the results of biclustering algorithms. The technique is based on a force-directed graph where biclusters are represented as flexible overlapped groups of genes and conditions.

::DEVELOPER

The VisUsal (Visual Analytics and Information Visualization, Universidad de Salamanca) group

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

BicOverlapper

:: MORE INFORMATION

Citation

BicOverlapper 2.0: visual analysis for gene expression.
Santamaría R, Therón R, Quintales L.
Bioinformatics. 2014 Jun 15;30(12):1785-6. doi: 10.1093/bioinformatics/btu120

Santamaría, R.; Therón, R. & Quintales, L.
BicOverlapper: A tool for bicluster visualization.
Bioinformatics, 2008, 24, 1212-1213

Treevolution 1.2 – Visual Analysis of Phylogenetic Trees

Treevolution 1.2

:: DESCRIPTION

Treevolution is a Java tool for the representation and exploration of phylogenetic trees that facilitates visual analysis. There are several useful tools to visualize phylogenetic trees, but their level of interaction is usually low, especially in the case of radial representations. Highly interactive visualizations can improve the exploration and understanding of phylogenetic trees. Treevolution implements strategies to interact with phylogenetic trees in order to allow a more thorough analysis by users.

::DEVELOPER

The VisUsal (Visual Analytics and Information Visualization, Universidad de Salamanca) group

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Windows / Mac OsX
  • Java

:: DOWNLOAD

Treevolution

:: MORE INFORMATION

Citation

Santamaría R. and Therón, R.
Treevolution: visual analysis of phylogenetic trees.
Bioinformatics, 2009, 25, 1970-1971

PLOTREP – Visual Analysis of Dispersed Genomic Repeats

PLOTREP

:: DESCRIPTION

PLOTREP is designed to be used by anyone who would like to identify interspersed repetitive elements in BAC-sized or smaller genomic regions. PLOTREP can merge fragments belonging to the same copy of a repeat and allows rapid visual inspection of the results via a dot-plot like two-dimensional graphical output.

::DEVELOPER

Agricultural Biotechnolog Center, Gödöllő, Hungary

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 available on request.

:: MORE INFORMATION

Citation

Tóth G, Deák G, Barta E, Kiss GB (2006)
PLOTREP: a web tool for defragmentation and visual analysis of dispersed genomic repeats.
Nucleic Acids Res. 34(Web Server Issue): W708-W713.

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