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Credit: Christoph Bock
Computer scientists have developed a web-based tool that allows researchers to visualize and compare large amounts of genomic information from high-throughput sequencing experiments.
The group described the tool, called Epiviz, in Nature Methods.
“Prior tools limited visualization to presentation and dissemination, rather than a hybrid tool integrating interactive visualization with algorithmic analysis,” said Héctor Corrada Bravo, PhD, of the University of Maryland in College Park.
Dr Corrada Bravo and his colleagues developed Epiviz, a web-based genome browser that integrates with the widely used, open-source Bioconductor analysis software through its Epivizr Bioconductor package.
Epiviz supports many popular next-generation sequencing techniques, such as ChIP-seq, RNA-seq, and DNA methylation analyses.
The tool also implements multiple visualization methods for location-based data (such as genomic regions of interest) and feature-based data (such as gene expression).
For example, because display objects are mapped directly to data elements, Epiviz links data across different visualizations, giving users visual insights of the spatial relationships of multiple data sets. The tool is designed to allow biomedical scientists to easily incorporate their own visualizations.
In the Nature Methods paper, Dr Corrada Bravo and his colleagues describe how they used Epiviz to visualize and analyze DNA methylation and gene expression data in colon cancer.
Using Epiviz and Bioconductor, the team found consistent regions of DNA methylation changes in colon cancer samples generated by the Cancer Genome Atlas project and similar gene expression in these regions of DNA methylation changes in other cancer types.
The results were in agreement with previous experiments showing DNA methylation changes across large regions in the colon cancer genome. 
Credit: Christoph Bock
Computer scientists have developed a web-based tool that allows researchers to visualize and compare large amounts of genomic information from high-throughput sequencing experiments.
The group described the tool, called Epiviz, in Nature Methods.
“Prior tools limited visualization to presentation and dissemination, rather than a hybrid tool integrating interactive visualization with algorithmic analysis,” said Héctor Corrada Bravo, PhD, of the University of Maryland in College Park.
Dr Corrada Bravo and his colleagues developed Epiviz, a web-based genome browser that integrates with the widely used, open-source Bioconductor analysis software through its Epivizr Bioconductor package.
Epiviz supports many popular next-generation sequencing techniques, such as ChIP-seq, RNA-seq, and DNA methylation analyses.
The tool also implements multiple visualization methods for location-based data (such as genomic regions of interest) and feature-based data (such as gene expression).
For example, because display objects are mapped directly to data elements, Epiviz links data across different visualizations, giving users visual insights of the spatial relationships of multiple data sets. The tool is designed to allow biomedical scientists to easily incorporate their own visualizations.
In the Nature Methods paper, Dr Corrada Bravo and his colleagues describe how they used Epiviz to visualize and analyze DNA methylation and gene expression data in colon cancer.
Using Epiviz and Bioconductor, the team found consistent regions of DNA methylation changes in colon cancer samples generated by the Cancer Genome Atlas project and similar gene expression in these regions of DNA methylation changes in other cancer types.
The results were in agreement with previous experiments showing DNA methylation changes across large regions in the colon cancer genome.
Credit: Christoph Bock
Computer scientists have developed a web-based tool that allows researchers to visualize and compare large amounts of genomic information from high-throughput sequencing experiments.
The group described the tool, called Epiviz, in Nature Methods.
“Prior tools limited visualization to presentation and dissemination, rather than a hybrid tool integrating interactive visualization with algorithmic analysis,” said Héctor Corrada Bravo, PhD, of the University of Maryland in College Park.
Dr Corrada Bravo and his colleagues developed Epiviz, a web-based genome browser that integrates with the widely used, open-source Bioconductor analysis software through its Epivizr Bioconductor package.
Epiviz supports many popular next-generation sequencing techniques, such as ChIP-seq, RNA-seq, and DNA methylation analyses.
The tool also implements multiple visualization methods for location-based data (such as genomic regions of interest) and feature-based data (such as gene expression).
For example, because display objects are mapped directly to data elements, Epiviz links data across different visualizations, giving users visual insights of the spatial relationships of multiple data sets. The tool is designed to allow biomedical scientists to easily incorporate their own visualizations.
In the Nature Methods paper, Dr Corrada Bravo and his colleagues describe how they used Epiviz to visualize and analyze DNA methylation and gene expression data in colon cancer.
Using Epiviz and Bioconductor, the team found consistent regions of DNA methylation changes in colon cancer samples generated by the Cancer Genome Atlas project and similar gene expression in these regions of DNA methylation changes in other cancer types.
The results were in agreement with previous experiments showing DNA methylation changes across large regions in the colon cancer genome.