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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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Can I run AUCell with my own list of regulons? #53

Closed fransilvion closed 5 years ago

fransilvion commented 6 years ago

Hi,

If I already have my own list of TFs and their targets from some external resource (RegNetwork for example), can I use it with AUCell and skip GENIE3 and enrichment step? If yes, how can I do it?

Also, can I use SCENIC output for pseudotime construction to see how activity of TFs is changing on pseudotime axis?

Thanks

s-aibar commented 5 years ago

Dear @fransilvion,

Yes, with AUCell you can use any type of gene set (e.g. TFs and potential target genes, pathway... etc, examples in the AUCell vignette). Once you have the AUC matrix, you can also choose to continue SCENIC's workflow (e.g. binarization, heatmap... etc) or use it as input for dimensionality reduction methods such as t-SNE/UMAP or pseudotime/trajectory inference. Of course, you will just need to adjust the interpretation of the results according to the input gene-sets...