search

pinellolab / STREAM

STREAM: Single-cell Trajectories Reconstruction, Exploration And Mapping of single-cell data
http://stream.pinellolab.org
GNU Affero General Public License v3.0
169 stars 45 forks source link

How to incorporate other motif databases aside from JASPAR in STREAM analysis of scATAC dataset #79

Open sylestiel opened 4 years ago

sylestiel commented 4 years ago

Hi,

How can I incorporate homer pwms motif list and mouse pwms v2 list into the STREAM_scATAC-seq-motif.ipynb?

Thanks! SH

huidongchen commented 4 years ago

What do you mean by 'incorporating'? How are you planning to use them?

sylestiel commented 4 years ago

I want the program to be able to scan for motifs that are not present in the JASPAR database. I think the motif ipynb only scans 128. I want to increase the repertoire. Hence have it scan other motif databases.

SH

huidongchen commented 4 years ago

Thanks for clarifying the problem! The short answer is that in STREAM we are not supporting other motif databases except for JASPAR2016 yet.

But that's something definitely on our to-do-list. In STREAM we are internally calling chromVAR (an R package) to scan and score motifs. We still need to further check and test the compatibility of these databases with our python dependencies before adding them. But hopefully we will include more motif collections very soon. Stay tuned!

sylestiel commented 4 years ago

Okay. Thanks!

On June 29, 2020 at 10:07 AM Huidong Chen notifications@github.com wrote:

Thanks for clarifying the problem! The short answer is that in STREAM we are not supporting other motif databases except for JASPAR yet.

But that's something definitely on our to-do-list. In STREAM we are internally calling chromVAR (an R package) to scan and score motifs. We still need to further check and test the compatibility of these databases with our python dependencies before adding them. But hopefully we will include more motif collections very soon. Stay tuned!

—
You are receiving this because you authored the thread.
Reply to this email directly, view it on GitHub https://github.com/pinellolab/STREAM/issues/79#issuecomment-651146087 , or unsubscribe https://github.com/notifications/unsubscribe-auth/APKOIKPIWJWEZ3LUKSUPHPLRZCN33ANCNFSM4OIZVL5A .