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aertslab / iRegulon

A regulon consists of a transcription factor (TF) and its direct transcriptional targets, which contain common TF binding sites in their cis-regulatory control elements. The iRegulon plugin allows you to identify regulons using motif and track discovery in an existing network or in a set of co-regulated genes.
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Iregulon tutorial for windows #1

Open saeedfc opened 4 years ago

saeedfc commented 4 years ago

Dear,

I tried to use Iregulon on Cytoscape in Windows. The tutorial given is mac based or on an old version of cytoscape. I did not even succeed in uploading the input. If I do it as import from file option, still I don't see a way to annotate it as source interaction. (I was using the hypoxia geneset file downloaded from the tutorial webpage) Can you kindly let me know, how to input the file in the new cytoscape on windows.

Thanks and kind regards. Saeed

ghuls commented 4 years ago

You need to add your column with gene names as source (green circle). If you don't have a header, also check Advanced Options....

Screenshot from 2019-08-19 10-29-27 Screenshot from 2019-08-19 10-32-12 Screenshot from 2019-08-19 10-29-57

saeedfc commented 4 years ago

Dear,

Thanks for the quick response. I am trying on windows. The interface is slightly different. If I understand correctly, the input will be a list of genes. I downloaded the list as given on the tutorial webpage. Attached is a pptx file with screen shots. I went the way you suggested. However, I can see that there are nodes (=0) and I cannot click on submit(inactive). Iregulon.pptx

ghuls commented 4 years ago

Once the gene network i drawn, you have to select all genes (or all genes you want) before going to Predict regulators and targets.

athan-dial commented 3 years ago

I am facing a similar issue. After uploading the hypoxia_geneset.txt file from the tutorial and selecting them as a source node, I get stuck permanently with the message Waiting until other jobs are finished...

ghuls commented 3 years ago

@athan-dial It should be working again.

athan-dial commented 3 years ago

Can confirm its fixed. Thank you!