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aertslab / SCENIC

SCENIC is an R package to infer Gene Regulatory Networks and cell types from single-cell RNA-seq data.
http://scenic.aertslab.org
GNU General Public License v3.0
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how to apply SCENIC to another species except for human,mouse and fly #111

Closed yangmeili1 closed 2 years ago

yangmeili1 commented 4 years ago

I read the introduction part about applying SCENIC into another species. It suggests us to download cis element database and other settings. But I am still confused. Could you give some more details or some specific procedures about it ? Thank you very much.

Yichel518 commented 3 years ago

Hello! Have you solved this problem? I have a similar problem for zebrafish recently...

s-aibar commented 2 years ago

Hello,

We have now created a tutorial on how to create new databases, which can be used to create databases for new organisms:

https://github.com/aertslab/create_cisTarget_databases

I hope this helps

k326xh commented 2 years ago

Hi @s-aibar,

Thanks for the info! I've followed the tutorial and generated zf1.genes_vs_motifs.rankings.feather for zebrafish. May I ask how to bypass the requirement in initializeScenic() that 'org' should be one of: mgi, hgnc, dmel?

SJagot commented 1 year ago

Hi,

I really want use SCENIC on my dataset but i'm also works on another species. I've followed the tutorial too and generated cisTarget_databases but i'm also stopped at the initializeScenic step. Is there any solution ?

jiangpuxuan commented 1 week ago

in initializeScenic() that 'org' should be one of: mgi, hgnc, dmel

I also struck at that step