Epiviz: a view inside the design of an integrated visual analysis software for genomics

BMC Bioinformatics
Florin Chelaru, Héctor Corrada Bravo

Abstract

Computational and visual data analysis for genomics has traditionally involved a combination of tools and resources, of which the most ubiquitous consist of genome browsers, focused mainly on integrative visualization of large numbers of big datasets, and computational environments, focused on data modeling of a small number of moderately sized datasets. Workflows that involve the integration and exploration of multiple heterogeneous data sources, small and large, public and user specific have been poorly addressed by these tools. In our previous work, we introduced Epiviz, which bridges the gap between the two types of tools, simplifying these workflows. In this paper we expand on the design decisions behind Epiviz, and introduce a series of new advanced features that further support the type of interactive exploratory workflow we have targeted. We discuss three ways in which Epiviz advances the field of genomic data analysis: 1) it brings code to interactive visualizations at various different levels; 2) takes the first steps in the direction of collaborative data analysis by incorporating user plugins from source control providers, as well as by allowing analysis states to be shared among the scientific community; 3) combine...Continue Reading

References

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Citations

Mar 13, 2018·Nucleic Acids Research·Justin WagnerHéctor Corrada Bravo
Sep 4, 2015·BMC Bioinformatics·Jan AertsDaniel Weiskopf

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Methods Mentioned

BETA
RNAseq
RNA-seq

Software Mentioned

R
Shiny
edgeR
WebGL
minfi
Gene Expression Barcode
Epiviz
limma
Cuffdiff
DiffBind

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