search

biolab / orange3-bioinformatics

🍊🔬 Bioinformatics add-on for Orange3
GNU General Public License v3.0
20 stars 21 forks source link

Export results of Gene Set Enrichment #309

Closed brainy-ninja closed 1 year ago

brainy-ninja commented 2 years ago

What's your use case?

I'm analyzing sets of genes for common biology. I import a list from an excel file, select specific columns and rows, then feed the results to the Genes widget. From there, I feed those genes into the Gene Set Enrichment widget. Everything runs fine and I can validate the results using a different tool. Now I want to export the list of pathways identified by the Gene Set Enrichment widget. When I save, it only saves the genes in the pathways, not the pathways themselves. When I open the data window and select rows to copy and paste into excel, this fails. I want to be able to save the pathways, which are the actual gene sets.

Big frustration. And also a problem since the actual results of the analysis are not saveable.

I think I did a good job in the first section. I am trying to do Venn overlaps of functional biological pathways enriched in transcriptomic datasets from either patient data or in experimental models of disease. I don't need to know which genes as a whole are represented in the sets. I need the pathways themselves and the subsets of genes in those pathways that come from my initial list..

What's your proposed solution?

Add additional outputs to the widget and/or enable copy/paste from the data viewer in the widget.

Are there any alternative solutions?

Manually on the web using g:Profiler and exporting to CSV.

JakaKokosar commented 1 year ago

This was addressed in https://github.com/biolab/orange3-bioinformatics/pull/322 and will be available in the next release.