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saezlab / decoupleR

R package to infer biological activities from omics data using a collection of methods.
https://saezlab.github.io/decoupleR/
GNU General Public License v3.0
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scRNA TF activity inference #117

Closed SofyaMa closed 4 months ago

SofyaMa commented 4 months ago

Great idea to extend the package to sc-data. I am trying to apply it to may Seurat object, however the run_uml function does not terminate. At least not within 24 hours.... do you know what I could do to speed up the TF activity inference. I am following the standard tutorial , please find my code attached.. any help is appreciated :D 

load("~/scRNA/data/merged_seurat.RData")
#PKN with TFs 
net <- get_collectri(organism='human', split_complexes=FALSE)
# Extract the normalized log-transformed counts
mat <- as.matrix(merged_seurat@assays$RNA@data)

# Run ulm
acts <- run_ulm(mat=mat, net=net, .source='source', .target='target',
                .mor='mor', minsize = 5)
acts
SofyaMa commented 4 months ago

or other question: can I somehow parallelize this function ?

PauBadiaM commented 4 months ago

Hi @SofyaMa,

It might be the case that you are running an old version of decoupleR. You could try installing the latest from GithHub:

remotes::install_github('saezlab/decoupleR')

Or you could try the python version of the package which is optimized to work with large sc atlases. Hope this is helpful!