Really great free software

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

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.



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.