Keren Zhou

icon indicating a website link https://scholar.google.com/citations?user=9G_ibwIAAAAJ&hl=en

icon company St. Jude Children's Research Hospital icon location Memphis

Results 25 comments of Keren Zhou

How to generate data_repo for hg38 genome?

Hi Viraj and Jens, Is the `data_repo` for `GRCh38` available now? Thanks, Keren

Can I apply cisTarget to estimate the RBP-regulon?

> SCENIC is designed for doing motif enrichment of proteins that bind to DNA (transcription factors), so using it for RBPs probably does not make much sense. Thank you for...

Can I apply cisTarget to estimate the RBP-regulon?

> You will need to change at least the the first step of pySCENIC (gene regulatory network) with something that makes sens for RBPs. > > Probably you are aware,...

Can I apply cisTarget to estimate the RBP-regulon?

> If you know which RBPs bind to which targets, you won't need the GRN related code of pySCENIC as there the TF to target gene relation is inferred and...

Can the input motifs be in the PWM format?

> The motifs need to be in Cluster-Buster format. > > The following function will create them (put one homer motif per file). > > ```shell > homer_to_clusterbuster () {...