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Is There Any Tools/Libraries To Use For Visualizing Genomic Feature Data In The Browser?

I have a genomic data in CSV or spreadsheet format(as table) (ex. A_niger_CBS_513_88 )with gene model/ protein domain architecture.

What libraries/tools that allow me to visualize the data (and to add my own tracks of data easily) ? I need something for using it with HTML5 ( web-based tools ) if there is nothing it is ok for desktop tools..

genome genome-browser visualization
• 7,375 views • link
updated by Chase Miller Chase Miller • written by inadamj • inadamj

3 answers

You can create a custom genome hub for the UCSC genome browser with your data: http://genome.ucsc.edu/goldenPath/help/hgTrackHubHelp.html

If needed the required files can be hosted on a site like: http://github.com see my blog http://plindenbaum.blogspot.fr/2013/07/playing-with-ucsc-genome-browser-track.html

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written by Pierre Lindenbaum Pierre Lindenbaum

Thanks @Pierre I will try to apply your suggestion and see what happens.

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written by inadamj • inadamj

As I understand you create an XML file then convert it to xsl then send it to UCSC then retrieve the output ??

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written by inadamj • inadamj

no, I wrote a xml file to generate all the files I wanted. But you can do this by hand ( create a fasta file, create a bigbed file... etc...).

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written by Pierre Lindenbaum Pierre Lindenbaum

Not sure if this is exactly what you are looking for. I wrote a html tool for visualizing gene feature/domain data here: http://www.nextgenetics.net/tools/anno_view/annotator.html

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written by Damian Kao Damian Kao

:) it seems close to what I should do >> could you pleas tell me how can I create something like this .. which tools\libraries ..etc

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written by inadamj • inadamj

For the visualizations/DOM manipulations I used d3.js. For the buttons/menus/checkboxes.. I wrote a MVC (model-view-controller) framework from scratch. Although I learned a lot about how the MVC pattern worked, I don't recommend writing it from scratch. You can use backbone.js or angular.js for MVC. I've also read some very cool things about the new react.js from Facebook (it implements a virtual DOM for faster page rendering).

If you want to hack something together fast, learn jquery, backbone.js, d3.js. Those 3 should be enough to create something similar.

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written by Damian Kao Damian Kao

I know about jQuery .. I am not interested to start from the scratch I want to edit some of the available features such as showing the images in SVG format and customize the output. if there is available plugin or library for the genome data that will be great for me.

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written by inadamj • inadamj

Scribl is a javascript HTML5 (canvas-based) genomic visualization library. Examples of both code and visualizations are on the home page

http://chmille4.github.io/Scribl/

• 267 views • link
written by Chase Miller Chase Miller

Do you have an idea about an SVG based or is there any possibility to convert it to SVG?

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written by inadamj • inadamj

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