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One of R's best features

Posted on 13, Mar, 2012 by in

.. has to be ggplot2, and I nearly missed the new version. It adds a number of new plots, cleans up the handling of labels and axis transformations, and allows us to finally add photos of team members to graphs:

One of R's best features

Visualizing genomic alterations

Posted on 09, Mar, 2012 by in

Stumbled over the Gitools framework on the Vizbi 2012 conference site their tools for visualizing and manipulating information on genomic alterations look particularly useful:

One of the advantages of having different dimensions in the same heatmap, like for example Copy Number Alterations (CNA) and Expression in the same file, is that after filtering or sorting on one dimension (e.g. CNA) it is possible to observe the effect of this filtering or sorting on another (gene expression changes).

We have been looking into the distribution of variants across pathways independently, but being able to automatically filter for mutually exclusive mutations should make our lives easier:

The rationale behind that observation is that once a gene involved in a particular critical pathway is altered, a second alteration affecting the same pathway does not confer a further selective advantage to the cancer cell.

Visualizing genomic alterations