search

aertslab / pySCENIC

pySCENIC is a lightning-fast python implementation of the SCENIC pipeline (Single-Cell rEgulatory Network Inference and Clustering) which enables biologists to infer transcription factors, gene regulatory networks and cell types from single-cell RNA-seq data.
http://scenic.aertslab.org
GNU General Public License v3.0
439 stars 181 forks source link

AUCellApp in PySCENIC? #71

Open fransilvion opened 5 years ago

fransilvion commented 5 years ago

Hi,

Does PySCENIC have anything similar to plotTsne_AUCellApp function in R version?

if not, is there any option to transfer PySCENIC results (say, auc matrix and regulons) to R SCENIC object? So I can visualize tSNE-plots with AUC thresholds and so on?

Thanks!

cflerin commented 5 years ago

Hi,

The R version does indeed have more plotting functionality. If you're familiar with the plotTsne_AUCellApp function in R, then you can import the pySCENIC output into R. The easiest way to do this would be to use the loom format produced by pySCENIC, then import this into R by using SCopeLoomR, which can read the regulons and the AUC matrix from the loom file.