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.
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.