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Hello,
I am trying to run this function on my dataset runSCENIC_4_aucell_binarize and I get this error :
Binary regulon activity: 26 TF regulons x 74626 cells.
(26 regulons including 'extended' …
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Dear author,
![image](https://github.com/aertslab/pySCENIC/assets/44579368/acca66f2-df2c-4ea1-8fea-06f61f868642)
```
Traceback (most recent call last):
File "/work/home/acp0wc9bsx/miniconda3/e…
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Many SCENIC jobs are very long running and a user can wonder if progress is being made. Having a mechanism to track progress would be very useful.
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Hello all,
thanks for the great package.
I am having issues running the aucell part of your tutorial more specifically line 45:
!pyscenic aucell \
{f_loom_path_scenic} \
reg.csv \
…
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Hi,
I am having a hard time preparing my Seurat object for input to SimiC's pipeline. Is there any code you can share about how you created the .pickle file for the DGE matrix that has cell barcode…
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Hi guys,
I have opened a loom file on scanpy by running: sc.read_loom. Once i try to see what is in there this is what pops up:
AnnData object with n_obs × n_vars = 56902 × 17473
obs: 'Age…
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Thanks for your recent update !
I have a question about the parallel computing about pySCENIC.
Recently, I'm using the singularity to run the image "aertslab-pyscenic-0.12.0.sif". In the first…
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**Describe the bug**
A clear and concise description of what the bug is.
Hi
Previously, I run mm9 on R scenic no problem.
I just first time try the pySCENIC on my own desktop. The process is exact…
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Can any one help me with a hint why I cannot read fully in output from pySCENIC in to Rstudio? I used pyCENIC to run the SCENIC workflow and I used the following command
`(base) charles@rahul-SYS-7…
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I get the following error while trying to run AUCell step from the tutorial (http://htmlpreview.github.io/?https://github.com/aertslab/SCENICprotocol/blob/master/notebooks/PBMC10k_SCENIC-protocol-CLI.…