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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 run SCENIC for chimp data? #182

Closed weishwu closed 2 years ago

weishwu commented 3 years ago

Hi,

I've seen papers in which they ran SCENIC on non-human primate sequencing data using human reference: https://www.nature.com/articles/s41467-020-15997-0#Sec8 https://www.cell.com/cell/pdf/S0092-8674(20)30056-8.pdf

I currently want to run SCENIC on chimpanzee 10x data and wonder if I need to modify any of the reference data files used by SCENIC and how, such as:

  1. refseq-r80__10kb/500bp_up_and_down_tss.mc9nr.feather
  2. TF file
  3. Motif database

Thanks,

s-aibar commented 2 years ago

Hello, We have now some tutorials to create databases with new settings: https://github.com/aertslab/create_cisTarget_databases These can also be used for new organisms.

I hope this helps