Michael Walker edited EPI View.md  about 9 years ago

Commit id: 4575cab762481783c9a9d768d2f78c098983dd8a

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The Problem  ----------  This team developed a simple and highly visually effective software package to display produce a  genetic and epigenetic marks, display,  allowing the user to view many different layers of information at once, and to easily switch between viewing a single region of one gene, toviewing  many genes, and even a whole chromosome. There are many publicly available datasets that could be used to create such visualisation software.   While there were systems, each with its own pros and cons, for viewing such data already available (e.g. Galaxy, UCSC Genome Browser, IGV, SeqMonk), none provided a holistic view of the data that allows optimal visualisation.  

Due to transformational changes in the way we examine these marks throughout the whole genome, biologists are creating a wealth of data that reports not only the DNA sequence, but also the amount of various epigenetic marks, and the amount of different factors bound to the DNA throughout the whole genome. This landslide of data is highly complex, and difficult for bench biologists to interrogate.  By visualising the genome and and in particular  its histone epigenetic  profile in a Circos plot, biologists are then able to interrogate the data through an intuitive interface. The web-based implementation allows the user to select the desired dataset, chromosomes, and which parts of the genome data to display.    Application/Relevance  -------  Pretty genome pictures!  Datasets  ------- 

Tech stack  ------  We used various Epiview is based on the  R libraries (RCircos)  Shiny \emph{RCircos},  to interact with R generate the Circos plots, and \emph{Shiny}, to be operable  via web page the web. This is enhanced by  D3.js to enhance Shiny generated web page for dynamic and interactive visualisation facilitate interactivity.  Future functionality  --------