Few months ago, Xavi and Michi wrote a post titled SVGmap: Configurable image browser for experimental data, which described a new tool developed in our lab. SVGmap is useful to create browsers for individualized high-quality images which change the color of some regions according to some values. For example, let’s say that you have expression data for various cell types in a particular tissue (or for various tissues in Drosophila, as in the image), you can draw an SVG image of the tissue showing each of the cell types and provide a tabulated file with the expression data, after few steps you can have a browser that allows you to search for particular genes and display the SVG image with the colors corresponding to the expression of each gene for each cell type. You can see some examples in the SVGmap web.
IntOGen Biomart portal
The DATABASE Oxford Journal has published a new volume in September dedicated to Biomart related databases and tools.
We have had a Biomart portal for IntOGen data since 2010 and we were invited to write a manuscript describing it. Read the rest of this entry »
Gitools published in PLoS ONE
About three years ago I started developing Gitools as an internal tool for people in the lab. We needed it to explore the results generated in IntOGen. It kept growing rapidly thanks to the feedback of group members. Read the rest of this entry »