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by ivan

A few curious papers.

April 3, 2014 in Ivan's Blog, Labwide Announcements

Here are a few intereseting recent development that have happened in the past week:

1) The paper I would like to talk about next Thursday: http://www.pnas.org/content/early/2014/03/19/1220873111

2) A paper about "machine teaching": http://www.tandfonline.com/doi/abs/10.1080/09540091.2014.885279#.Uz3HInXqfbg

3) A paper on differential gene expression detection: http://www.biomedcentral.com/1471-2105/15/79

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by ivan

Short update on the Palantir visualization

September 26, 2013 in Ivan's Blog

I have put together a simplistic R script that draws a few circles next to the branches on a tree.

Screenshot - 09252013 - 06:27:27 PM
Thus far, it is a rather simple hack that uses a the obscure numbering of branches provided by APE. I foresee that it might be necessary to come up with a better way to encode branch identity. This really depends on what the output from Palantir is.

Another problem is that I am using the plotrix library for drawing things. Sadly, it does not scale well when a window is resized, so you might end up with elliptical circles. Additionally, I will have to play with the coordinates of the circle offsets to make sure they consistently fit on the picture.

Hopefully, when I get the data, it will not be too hard to make work properly.

The current usage information is provided in the repository description.

 

 

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