Tag Archives: rstudio

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What’s the Answer? (creating a web site to visualize a paper’s results)

reddit_iconThis week’s highlighted question is from the Bioinformatics subreddit. It’s a question about display of your research data for others to access and interact with. I think this will be an issue more and more as huge data sets become available, on a wide range of topics, none of which will fit in to traditional publications. Sometimes there will be data repositories (and I hope that when an appropriate repository is available data will also go there still). But I can imagine some projects that have more or different features than some existing repository. So they may want to provide a place for people to interact with their data above and beyond just download access. So this discussion was interesting to me.

In addition, just yesterday I talked about the ZBrowse tool that sits on top of R and RStudio as commenters discuss here for other situations as well. And if you try out ZBrowse you’ll see some similarity in the software features to the kidney metabolism interface that’s discussed in the replies.

Of course, maintenance over the long run is still an issue. But some of those concerns are possibly being managed better with Docker, Bioboxes, and other strategies for data management and storage that funding agencies are scrutinizing. Or, at least it’s being noticed that these issues need real strategies and oversight.

reddit question icon Creating website for data visualisation?

I’m submitting a paper soon, and we are thinking about providing a website for visualisation of results. (Reading data from a table and then providing graphs and a statistics table for a gene of interest etc)

Is anyone familiar with this process? Any suggestions? And how long will this take to learn and implement.. I’m familiar with bash, R and a bit of python syntax, if that helps

Any advice appreciated!

–willgotskill

Have a look at the discussion threads. I thought it was interesting and worth knowing about how people are solving this.

ZBrowse sample image

Video Tip of the Week: ZBrowse for GWAS viewing and exploration

Maybe you’ve heard of the others. ABrowse. BBrowse. CBrowse. [you get the idea] GBrowse has been widely adopted. JBrowse is picking up steam. Into the orderly arrangement we now throw ZBrowse: a new way to look at genome-wide association study data.

Sharing and chatter about ZBrowse for viewing GWAS was abundant when the paper was published recently.

I could see the appeal immediately. One of the first things I check when exploring new software is the species range. See, I’m agnostic on species, and especially like to find tools that support a wide range of species. ZBrowse does this. Right in their paper they provide a chart comparing their features to other tools, and that tidbit jumped right out at me.

Although we usually like to highlight web-based tools, this one was really different and worth covering even though it requires you to do a bit more lifting on installing it. But they help with that, in their videos and instructions. And ultimately it runs in your browser, once you’ve got the right pieces in place. I was able to set it up and run it (after updating my R and RStudio).

I’m going to skip the installation and data loading videos for now, but you should go over and see them when you are ready to try it out. I’ll just give you a look at the features they show in their introductory video for the browser part. That will give you the best idea of why it’s worth trying it out.

It does require you to have R installed, and RStudio. We’ve talked about both of those before, but if they are new to you, check’em out in these other Video Tips of the Week: Introduction to R Statistical Software, RStudio as an Interface for using R.

It comes loaded with some plant data, but you can use other data you have. It was very easy to look at the Manhattan plot view, and then focus on smaller chosen regions. I really liked how easy it was to see what’s in the neighborhood of a selected item when you turned to the annotation tab. ZBrowse sample image

It might also be worth trying this out as a software delivery strategy–I was just reading about other folks who are offering tools that sit on top of R and RStudio this way (come back tomorrow for another example). People who want to offer you the chance to look over large data sets they are providing are considering this.

Quick links:

ZBrowse at Baxter Laboratory: http://www.baxterlab.org/#!/cqi0

R: http://www.r-project.org/

RStudio: http://www.rstudio.com/

References:

Fertig, E. (2012) Getting Started in R.

Racine J.S. (2011). RStudio: A Platform-Independent IDE for R and Sweave, Journal of Applied Econometrics, 27 (1) 167-172. DOI: http://dx.doi.org/10.1002/jae.1278

Ziegler, Greg R., Ryan H. Hartsock, and Ivan Baxter. “Zbrowse: an interactive GWAS results browser.” PeerJ Computer Science 1 (2015): e3. DOI: 10.7717/peerj-cs.3