The outputs are instable

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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The outputs are instable #221

Closed XinWang19 closed 2 years ago

XinWang19 commented 2 years ago

Hi,

I ran SCENIC on my single cell dataset (about 900 cells) twice, with a difference of 14 cells. However, I found there were considerable amount of regulons differing after I added these 14 cells (as following). How could I ensure the reproduciblity between the datasets? Thanks!

Xin

s-aibar commented 2 years ago

Dear @XinWang19 ,

This issue was addressed in https://www.nature.com/articles/s41596-020-0336-2 . At the moment the solution we recommend is to run SCENIC several times to assess the stability of the results. This is automated in VSN-pipelines (i.e. see "Scenic multiruns").

I hope this helps