BRB-ArrayTools 4.6.2 – Visualization & Analysis of DNA Microarray Gene Expression Data

BRB-ArrayTools 4.6.2

:: DESCRIPTION

BRB-ArrayTools is an integrated software package for the analysis of DNA microarray data.

BRB-ArrayTools contains utilities for processing expression data from multiple experiments, visualization of data, multidimensional scaling, clustering of genes and samples, and classification and prediction of samples. BRB-ArrayTools features drill-down linkage to NCBI databases using clone, GenBank, or UniGene identifiers, and drill-down linkage to the NetAffx database using Probeset ids.

::DEVELOPER

the Biometric Research Branch of the Division of Cancer Treatment & Diagnosis of the National Cancer Institute

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

BRB-ArrayTools

:: MORE INFORMATION

Citation

Analysis of gene expression data using BRB-ArrayTools.
Simon R, Lam A, Li MC, Ngan M, Menenzes S, Zhao Y.
Cancer Inform. 2007 Feb 4;3:11-7.

SharedHap 20150114 – Haplotype-sharing Visualization

SharedHap 20150114

:: DESCRIPTION

SharedHap computes and visualize Haplotype-Sharing Patterns among subjects of interests in a pedigree.

::DEVELOPER

Ellen M. Wijsman

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C
  • R

:: DOWNLOAD

 SharedHap

:: MORE INFORMATION

Citation:

Hum Hered. 2014;78(1):1-8. doi: 10.1159/000358171.
Visualization of haplotype sharing patterns in pedigree samples.
Kim S1, Saad M, Tsuang DW, Wijsman EM.

RiboSketch 0.8.2 – Visualization of multi-stranded RNA and DNA Secondary Structure

RiboSketch 0.8.2

:: DESCRIPTION

RiboSketch is a drawing program for the production of RNA and DNA secondary structure images.The user provides an input file (.ct, .bpseq, .dbn, or the save file type .rs) containing the sequence and base-pairing of the strand(s).

::DEVELOPER

Shapiro Group

:: SCREENSHOTS

n/a

:: REQUIREMENTS

  • Linux/Windows/MacOsX

:: DOWNLOAD

RiboSketch

:: MORE INFORMATION

Citation:

Lu JS, Bindewald E, Kasprzak WK, Shapiro BA.
RiboSketch: versatile visualization of multi-stranded RNA and DNA secondary structure.
Bioinformatics. 2018 Dec 15;34(24):4297-4299. doi: 10.1093/bioinformatics/bty468. PMID: 29912310; PMCID: PMC6289134.

ProCon 2.0 – Localization & Visualization of Protein Conservation

ProCon 2.0

:: DESCRIPTION

ProCon is tool for locating and visualization of evolutionary conservation in protein sequences. The method can identify three types of conservation: identity (type I), physicochemical similarity (II), and covariant conservation (III). The conservative sites of type I and II are located with entropy calculation and the third type is identified by calculation of mutual information. The interacting networks formed by covariant pairs can also be identified. All the three types of conservation can be visualized in a representative protein structure. The tool performs exhaustive analysis results of which can be used e.g. for identifying different types of conserved residues, studying protein-protein interactions, explaining consequences of disease-causing mutations and mutant design for protein engineering.

::DEVELOPER

ProCon Team

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Mac
  • Java

:: DOWNLOAD

 ProCon

:: MORE INFORMATION

HAIviz v.0.3 – Healthcare-associated infections Visualization tool

HAIviz v.0.3

:: DESCRIPTION

HAIviz is a single page application build to help you integrate and interactively visualize genomic epidemiological information of a local outbreak.

::DEVELOPER

Beatson Microbial Genomics Lab.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

NO

:: MORE INFORMATION

 

SplicingViewer 1.1.0 – Detection, Annotation and Visualization of the Alternative Splicing from RNA-Seq Data

SplicingViewer 1.1.0

:: DESCRIPTION

SplicingViewer is an integrated tool which can detect the splice junctions based on known gene models, annotate the alternative splicing patterns based on the splice junctions, and visualize the patterns of alternative splicing events. In addition, as a viewer, SplicingViewer can also be used to display the RNA-Seq reads mapping results with high speed and lower memory spend.

::DEVELOPER

SplicingViewer team

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux/ Windows/ MacOsX
  • Java

:: DOWNLOAD

 SplicingViewer

:: MORE INFORMATION

Citation

Genomics. 2012 Mar;99(3):178-82. doi: 10.1016/j.ygeno.2011.12.003. Epub 2011 Dec 28.
Detection, annotation and visualization of alternative splicing from RNA-Seq data with SplicingViewer.
Liu Q, Chen C, Shen E, Zhao F, Sun Z, Wu J.

Ontologizer 2.1 – Analysis and Visualization of High-Throughput Biological Data Using Gene Ontology

Ontologizer 2.1

:: DESCRIPTION

Ontologizer is a Java webstart application for GO term enrichment analysis that provides browsing and graph visualization capabilities. The Ontologizer allows users to analyze data with the standard Fisher exact test and also the parent-child method and topology methods.

::DEVELOPER

The Computational Biology @ Charité Berlin

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / MacOsX / Windows
  • Java

:: DOWNLOAD

  Ontologizer

:: MORE INFORMATION

Citation

Bioinformatics. 2008 Jul 15;24(14):1650-1. Epub 2008 May 29.
Ontologizer 2.0–a multifunctional tool for GO term enrichment analysis and data exploration.
Bauer S, Grossmann S, Vingron M, Robinson PN.

VISDA 1.0 – Visualization, and Discovery for Cluster Analysis of Genomic data

VISDA 1.0

:: DESCRIPTION

VISDA (VIsual and Statistical Data Analyzer) is a software for cluster modeling, visualization, and discovery in genomic data. VISDA performs progressive, coarse-to-fine (divisive) hierarchical clustering and visualization, supported by hierarchical mixture modeling, supervised/unsupervised informative gene selection, supervised/unsupervised data visualization, and user/prior knowledge guidance, to discover hidden clusters within complex, high-dimensional genomic data.

::DEVELOPER

Computational Bioinformatics & Bio-imaging Laboratory (CBIL)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 VISDA

:: MORE INFORMATION

Citation:

caBIG VISDA: modeling, visualization, and discovery for cluster analysis of genomic data.
Zhu Y, Li H, Miller DJ, Wang Z, Xuan J, Clarke R, Hoffman EP, Wang Y.
BMC Bioinformatics. 2008 Sep 18;9:383.

FluxViz/CyFluxViz 1.00 – Cytoscape Plugin for Flux Visualization

FluxViz/CyFluxViz 1.00

:: DESCRIPTION

FluxViz is an open-source Cytoscape plug-in for the visualization of flux distributions in molecular interaction networks.FluxViz was used for the visualization and analysis of the metabolic network of the human hepatocyte

::DEVELOPER

Matthias König

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

FluxViz

:: MORE INFORMATION

Citation:

Genome Inform. 2010 Jul;24(1):96-103.
Fluxviz – cytoscape plug-in for visualization of flux distributions in networks.
König M, Holzhütter HG.

GPViz 1.2.8 – Dynamic Gene-centered Visualization of Genomic Regions and/or Variants

GPViz 1.2.8

:: DESCRIPTION

GPViz (GeneProteinViz) is a versatile Java-based software for dynamic gene-centered visualization of genomic regions and/or variants. User defined data can be loaded in common formats as resulting from analysis workflows used in sequencing applications and studied in the context of the gene, the corresponding transcript isoforms, proteins and their domains or other protein features. Both the genomic regions and variants can be also defined interactively.

::DEVELOPER

the Division of Bioinformatics, Innsbruck Medical University

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows/Linux /MacOsX
  • Java

:: DOWNLOAD

  GPViz

:: MORE INFORMATION

Citation

Bioinformatics. 2013 Sep 1;29(17):2195-6. doi: 10.1093/bioinformatics/btt354. Epub 2013 Jun 19.
GPViz: dynamic visualization of genomic regions and variants affecting protein domains.
Snajder R1, Trajanoski Z, Hackl H.