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Hello, I have been trying to run pySCENIC and I went through all the steps as noted in your tutorial pretty easily, thank you for that.
But now I want to export to a .loom file, to be able to analy…
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i have completed up through creation of the df object via:
```
with ProgressBar():
df = prune2df(dbs, modules, MOTIF_ANNOTATIONS_FNAME,client_or_address="dask_multiprocessing")
```
then I get…
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I have a situation where the same TF shows up as both a positive and negative regulon in a given cluster of my cells (e.g. Prdm1, Runx2 in the red cluster). Does it just mean that some of its targets …
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1. I install according to this link: https://rawcdn.githack.com/aertslab/SCENIC/a0a00644b2f3589a3e2bc65486fc5f6cc00f48e1/inst/doc/SCENIC_Setup.html#sample-dataset-download-format
and run according t…
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Hi!
Thanks for building SCENIC, been helping alot in my research.
However I have been having trouble loading the feather database when I run step 2.
```
runSCENIC_2_createRegulons(scenicOptio…
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Hi all, i'm working on a single cell dataset with scenic, and i found a weird result: one TF, Atoh1, showed an adverse trend compared to its regulon:
I got target list of Atoh1 from output fo…
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Hi,
I'm using the SCENIC_2_createRegulons() function and keep getting the same error: all connection are in use. The detail is:
`runSCENIC_2_createRegulons(scenicOptions)
11:25 Step 2. Identi…
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Hi,
Could you explain how to interpret the heatmap? The dark part (close to 0) means the regulon not active? If so vast majority of cells have nonactive regulons.
Also, how to use binarize(auc_mtx…
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Hi,
Thanks for referring to the Drosophila eye development paper. I read through it. Excellent work!
For the co-expression network construction, the paper used PTM, and GENIE3. The current version …
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Hi,
I ran pySCENIC's workflow to generate AUC values followed by `AUC_exploreThresholds` from the latest version (1.2.4) of `AUCell`.
```
cells_assignment Error in { : task 386 failed - "miss…