Really great free software

Just discovered this great suite of tools for data mining and visualising data.

http://orange.biolab.si/

This is python based and you can add your own scripts to the tools. Very simple to use with  intuitive graphic user interface. The add-ons are also really useful with one specifically bioinformatic giving access to databases etc. Below is an example of how to do a heatmap. And you can output a beautiful high resolution heatmap.png.

heatmap_function

heatmap_screenshot

Working on visually presenting the results

I have been busy writing my thesis so no posts for a while. Interspersed with writing I have been finding ways to present the data. There are many ways to visualize the differential expression such as heatmaps and volcano plots. Both do-able in R, but I am now looking into some python modules that look promising.

Anyway here are volcano plots (using R) from DE expression between 0 and 48 hours post inoculation  (A) susceptible and (B) resistant plants. Each dot represents a transcript. Red =  FDR <0.01, Green = FDR<0.01 and l log2 fold change >4 , Yellow and labelled a-j= FDR< 1.00E-07 and log2 fold change >4 . Gene homologues labelled are; a = zinc finger protein, b,d = carboxylesterase 12, c = Puccinia psidii ITS, e = zinc finger CCCH domain-containing protein,  f= myosin heavy chain kinase, uncharacterized, g = metalloendoproteinase, h= strigolactone esterase.

volcano2