momur
momur
Hi Seppe, Thank you for your response. Here is how motif enrichment dict looks like. This is the output folder.
Hi @SeppeDeWinter , Thank you for your suggestions. I ran the codes and here are the outputs: It is weird that regions from scenic_obj doesnt start with "chr"
Hi @SeppeDeWinter I tried your suggestion. it still gives an error. I tried to run buid_grn but it gave this error: Thanks!
Hi @SeppeDeWinter , I did what you suggested. Here how scenic_obj looks like: Cistopic object also doesnt have "chr" in regions, should I change them as well? merged_signatures_direct and merged_signatures_extend...
Hi @SeppeDeWinter After your suggestion, I ran merge_cistromes and then repeat build_grn. This time it calculated more than usual. It produced "Cistromes" but no eRegulons
Hi @SeppeDeWinter Yes, I corrected `region_to_gene` and`search_space`. Everything looks consistent right now. I also ran `merge_cistromes` after the changes. I ran `build_grn`and it ran for a long time. I thought...
Hi @SeppeDeWinter Here are the outputs:
Hi @SeppeDeWinter Yes, you were right. Now I see there there is an error at the bottom "relevant_tfs is not defined"
It printed long list of TF names :
hmm I got this error when I ran `relevant_tfs, e_modules = create_emodules( SCENICPLUS_obj=scplus_obj,..` part