As you might know, Orange comes with several basic widget sets pre-installed. These allow you to upload and explore the data, visualize them, learn from them and make predictions. However, there are also some exciting add-ons available for installation. One of these is a bioinformatics add-on, which is our specialty.
Bioinformatics widget set allows you to pursue complex analysis of gene expression by providing access to several external libraries. There are four widgets intended specifically for this - dictyExpress, GEO Data Sets, PIPAx and GenExpress. GEO Data Sets are sourced from NCBI, PIPAx and dictyExpress from two Biolab projects, and finally GenExpress from Genialis. A lot of the data is freely accessible, while you will need a user account for the rest.
Once you open the widget, select the experiments you wish to use for your analysis and view it in the Data Table widget. You can compare these experiments in Data Profiles, visualize them in Volcano Plot, select the most relevant genes in Differential Expression widget and much more.
Three widgets with experiment data libraries.
These databases enable you to start your research just by installing the bioinformatics add-on (Orange → Options → Add-ons…). The great thing is you can easily combine bioinformatics widgets with the basic pre-installed ones. What an easy way to immerse yourself in the exciting world of bioinformatics!