GOrilla – Gene Ontology enRIchment anaLysis and visuaLizAtion tool

GOrilla

:: DESCRIPTION

GOrilla is a web-based application that identifies enriched GO terms in ranked lists of genes, without requiring the user to provide explicit target and background sets. This is particularly useful in many typical cases where genomic data may be naturally represented as a ranked list of genes (e.g. by level of expression or of differential expression).

::DEVELOPER

Yakhini Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Eran Eden, Roy Navon, Israel Steinfeld, Doron Lipson and Zohar Yakhini.
GOrilla: A Tool For Discovery And Visualization of Enriched GO Terms in Ranked Gene Lists“,
BMC Bioinformatics 2009, 10:48.

PIVOT 2.0 – Protein Interactions VisualizatiOn Tool

PIVOT 2.0

:: DESCRIPTION

PIVOT (Protein Interactions VisualizatiOn Tool) is a Java-based tool, for visualizing protein-protein interactions. It is rich in features that help the users navigate and interpret the interactions map, as well as graph-theory algorithms for easily connecting remote proteins to the displayed map.PIVOT is not limited to the data present in any database, but instead allows the users to create their own dataset, by importing any available lists of interactions and combining them together. PIVOT is currently configured to work with proteins from four different species (human, yeast, drosophila and mouse), and present functional annotations, designations of homologs from the four species, and links to information pages. The protein data is stored in an MS-Access file, easily modifiable by the users to enter their own data.

::DEVELOPER

Ron Shamir’s lab

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux / MacOSX
  • Java

:: DOWNLOAD

PIVOT

:: MORE INFORMATION

Citation

Bioinformatics. 2004 Feb 12;20(3):424-5.
PIVOT: protein interacions visualizatiOn tool.
Orlev N1, Shamir R, Shiloh Y.

BURRITO – Visualization Tool for Exploratory Data Analysis of Metagenomic data

BURRITO

:: DESCRIPTION

BURRITO is a web-based tool for interactive exploration of metagenomic datasets, linking taxonomic and functional microbiome profiles

::DEVELOPER

the Borenstein Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Web Server

:: DOWNLOAD

BURRITO

:: MORE INFORMATION

Citation

Front Microbiol. 2018 Mar 1;9:365. doi: 10.3389/fmicb.2018.00365. eCollection 2018.
BURRITO: An Interactive Multi-Omic Tool for Visualizing Taxa-Function Relationships in Microbiome Data.
McNally CP, Eng A, Noecker C, Gagne-Maynard WC, Borenstein E.

SNPtrio – SNP Trio Visualization tool

SNPtrio

:: DESCRIPTION

SNPtrio offers an additional category of information by visualizing and analyzing inheritance patterns in trios (mother, father, and child).

::DEVELOPER

the Pevsner Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C  compiler
  • R package

:: DOWNLOAD

  SNPtrio

:: MORE INFORMATION

Citation

Hum Mutat. 2007 Dec;28(12):1225-35.
Visualization of uniparental inheritance, Mendelian inconsistencies, deletions, and parent of origin effects in single nucleotide polymorphism trio data with SNPtrio.
Ting JC, Roberson ED, Miller ND, Lysholm-Bernacchi A, Stephan DA, Capone GT, Ruczinski I, Thomas GH, Pevsner J.

GenExp /DASgenexp – Web-based Visualization tool that interactively Explore Genomic Database

GenExp /DASgenexp

:: DESCRIPTION

GenExp is a web based and fully interactive visual DAS client. GenExp is a genome oriented DAS client capable of creating informative representations of genomic data zooming out from base level to complete chromosomes. It proposes a novel approach to genomic data rendering and uses the latest HTML5 web technologies to create the data representation inside the client browser.

 DASGenExp is a web-based visualization tool that interactively explore distributed DAS data bases.

::DEVELOPER

 the Algorithmics and Genetics Group

:: SCREENSHOTS

:: REQUIREMENTS

  • Firefox

:: DOWNLOAD

 No

:: MORE INFORMATION

Citation

GenExp: an interactive web-based genomic DAS client with client-side data rendering.
Gel Moreno B, Messeguer Peypoch X.
PLoS One. 2011;6(7):e21270. Epub 2011 Jul 5.

MoluCAD 1.034 – Molecular Modeling & Visualization Tool

MoluCAD 1.034

:: DESCRIPTION

MoluCAD is a full-featured molecular modeling and visualization tool designed for Windows. Originally conceived as an aid for students of organic chemistry, MoluCAD has quickly evolved into much more. The latest version incorporates many advanced features only found in expensive workstation-based modeling packages. Ease of use, premium graphical quality, and computational robustness are the trademarks of MoluCAD.

::DEVELOPER

New River Kinematics

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

MoluCAD

:: MORE INFORMATION

For more information, e-mail:  molucad@kinematics.com

Genomica 3.040710 – Analysis and Visualization Tool for Genomic data

Genomica 3.040710

:: DESCRIPTION

Genomica is an analysis and visualization tool for genomic data, which can integrate gene expression data, DNA sequence data, and gene and experiment annotation information.

::DEVELOPER

Segal Lab 

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux/ Windows/MacOsX

:: DOWNLOAD

 Genomica

:: MORE INFORMATION

 

eQTLexplorer 6.0 – eQTL Visualization tool

eQTLexplorer 6.0

:: DESCRIPTION

eQTLexplorer is an eqtl visualization tool that allows users to mine and understand data from a repository of genetical genomics experiments.

::DEVELOPER

Michael Mueller, Jon Mangion

:: SCREENSHOTS

::REQUIREMENTS

  • Linux/Windows/MacOsX
  • Java

:: DOWNLOAD

 eQTLexplorer

:: MORE INFORMATION

Citation

Mueller M et al. (2006)
eQTLexplorer: integrated mining of genetical genomics experiments.
Bioinformatics, 22: 509-11

zPicture / multi-zPicture – Dynamic Alignment & Visualization Tool

zPicture / multi-zPicture

:: DESCRIPTION

zPicture is a dynamic alignment and visualization tool that is based on blastz alignment program utilized by PipMaker. zPicture alignments can be automatically submitted to rVista 2.0 to identify conserved transcription factor binding sites.

multi-zPicture is a multi-sequence version of zPicture alignment and visualization tool.

::DEVELOPER

Miller Lab at Penn State University Center for Comparative Genomics and Bioinformatics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 zPicture

:: MORE INFORMATION

Citation:

Ivan Ovcharenko, Gabriela G. Loots, Ross C. Hardison, Webb Miller, and Lisa Stubbs
zPicture: Dynamic Alignment and Visualization Tool for Analyzing Conservation Profiles
Genome Res. 2004. 14: 472-477