AssociationViewer: a scalable and integrated software tool for visualization of large-scale variation data in genomic context

We present a tool designed for visualization of large-scale genetic and genomic data exemplified by results from genome-wide association studies. This software provides an integrated framework to facilitate the interpretation of SNP association studies in genomic context. Gene annotations can be ret...

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Bibliographic Details
Published in:Bioinformatics 2009-03, Vol.25 (5), p.662-663
Main Authors: Martin, Olivier, Valsesia, Armand, Telenti, Amalio, Xenarios, Ioannis, Stevenson, Brian J.
Format: Article
Language:English
Subjects:
Agglomeration
Applications Note
Biological and medical sciences
Computational Biology - methods
Computer programs
Databases, Genetic
Format
Fundamental and applied biological sciences. Psychology
General aspects
Genomics
Internet
Linkage Disequilibrium
Mathematics in biology. Statistical analysis. Models. Metrology. Data processing in biology (general aspects)
Repositories
Software
User-Computer Interface
Visualization
Windows (computer programs)
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Description
Summary:We present a tool designed for visualization of large-scale genetic and genomic data exemplified by results from genome-wide association studies. This software provides an integrated framework to facilitate the interpretation of SNP association studies in genomic context. Gene annotations can be retrieved from Ensembl, linkage disequilibrium data downloaded from HapMap and custom data imported in BED or WIG format. AssociationViewer integrates functionalities that enable the aggregation or intersection of data tracks. It implements an efficient cache system and allows the display of several, very large-scale genomic datasets. Availability: The Java code for AssociationViewer is distributed under the GNU General Public Licence and has been tested on Microsoft Windows XP, MacOSX and GNU/Linux operating systems. It is available from the SourceForge repository. This also includes Java webstart, documentation and example datafiles. Contact: brian.stevenson@licr.org Supplementary information: Supplementary data are available at http://sourceforge.net/projects/associationview/ online.
ISSN:1367-4803
1460-2059
1367-4811
DOI:10.1093/bioinformatics/btp017