mpiersonsmela

I had the exact same problem. I will try downloading https://resources.aertslab.org/cistarget/databases/homo_sapiens/hg38/refseq_r80/mc9nr/gene_based/hg38__refseq-r80__10kb_up_and_down_tss.mc9nr.genes_vs_motifs.rankings.feather and see if it works. You really should update the index page, I wasted a lot of time before...

The input command was: naive_new_reg

OK, I'll upload the example data tomorrow. Regarding the filtering, I'm removing all the loci that have zero reads for all samples in a group. This filtering strategy worked OK...

OK, I uploaded the files to your Dropbox link. I wasn't able to figure out how to take a small portion that replicates the results, so I just uploaded the...

Thanks! I'll follow up with you by email about collapsing strands.

Regarding collapsing strands, does this basically mean treating each CpG site as one genomic coordinate? I am not sure this would be appropriate for me, since I expect a substantial...

Agreed. UBB is definitely not a transcription factor.

It's 2023, and I still have the same question.