Epiviz

Epiviz

 3 is an interactive visualization tool for functional genomics data. It supports genome navigation like other genome browsers, but allows multiple visualizations of data within genomic regions using scatterplots, heatmaps and other user-supplied visualizations. It also includes data from the Gene Expression Barcode project for transcriptome visualization. It has a flexible plugin framework so users can add d3 visualizations. You can find more information about  3 at http://epiviz.github.io and see a video tour here.

The Epivizr Bioconductor package implements two-way communication between the R/Bioconductor computational genomics environment and  3. Objects in an R session can be displayed as tracks or plots on  3. Epivizr uses WebSockets for communication between the browser JavaScript client and the R environment, the same technology underlying the popular Shiny system for authoring interactive web-based reports in R.

Recent Posts

Epigenomic visualization in Nature Methods News and Comment

17 August 2015

Epiviz was highlighted in a recent Nature Methods News and Comment piece on visualization of epigenomic data.

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Architecture and design paper in Biovis '15

17 August 2015

Our paper detailing the architecture and design of Epiviz is now available on the BMC Bioinformatics site. It is published in a supplement containing a good number of...

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Using BED files with epiviz

18 December 2014

On a twitter exchange I showed A. Quinlan how to use epivizr to load data from a custom bed file. Here is the code I gave him:

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New epivizr release

31 October 2014

Version 1.4 of epivizr was released as part of the new Bioconductor 3.0 release. There are a good number of new features in epivizr in this release, including...

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New Code Customization Feature for Visualizations

28 October 2014

See it in  3

See it in  2

Now visualizations' code can be customized in the UI, based on user needs!

To do it, simply click...

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New Clustering Feature for Heatmap Plots

28 October 2014

See it in  3

See it in  2

We implemented a new Clustering feature in the Heatmap Plot! You can use it to group together measurements...

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Epiviz published in Nature Methods

03 August 2014

Our first paper describing the  3 system was published today in Nature Methods. From the abstract:

Visualization is an integral aspect of genomics data analysis. Algorithmic-statistical analysis...

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