Jeff Vierstra

Let me dig up the hierarchical.py script. The background file only has a marginal effect.

Try here: https://www.vierstra.org/resources/motif_clustering#v10-2020-4-14

The link between TF genes and motifs is a complicated one. Any motifs can be recognized by many TFs -- in fact Tim Hughes and Matt Wierauch have shown that...

The annotations that connect TF genes to motifs are messy (I largely lifted those annotations from CIS-PB). The gene names "tf_name" field in the metadata file correspond to the TF...

Thanks for pointing this out -- will get to this as soon as I have time.

Yes. These were added manually.

Have you found a work around? This works for me using miniconda and the included YML enviromental config file...

In principle, one could compute the expected cleavages for Tn5 data, however, 6mer sequence preference model should be trained on a Tn5 experiment from de-proteinized DNA (naked DNA). Another issue...