get_gene_activity

[TingTingShao]

Hi,

Could I please ask how get_gene_activity works. I can see it is calculated on the consensus regions. So the gene activity score is mostly distance based if I understand it correctly. The score of same gene for different cell/nuclei, I suppose it is different, and the difference is based on the openness of the region in each cell/nuclei?

Thanks,
tingting

[SeppeDeWinter]

Hi TingTing

This is based on this paper: https://www.nature.com/articles/s41586-021-04262-z#Sec8
See methods: "Gene accessibility matrix".

In summary, gene activity is based on:

• distance to the gene.
• Specificity of the peaks (gini score across cells).
• and accessibility of the peaks (per cell).

Does this help?

All the best,

Seppe

[TingTingShao]

Yes, it clarifies the question.

Thanks!
tingting