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**Describe the bug**
This is not a hard error, but it's an issue with the output of the analysis.
- For all the regulon markers including markers that should act in opposite directions the perturb…
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Dear authors, thank you for bringing us such a wonderful toolkit.
I have successfully implemented pyscenic, the retained TF-target and weight on regulon were retrieved and as input to cytoscape for …
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![c417a7a2f527b0657af819afe6f0b74](https://github.com/aertslab/pySCENIC/assets/110780219/8db6181e-97af-4496-8544-25b10062eaf2)
![1711077120810](https://github.com/aertslab/pySCENIC/assets/110780219/8…
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Hello,
I'm currently running the Docker version of pyscenic (0.12.1) on HPC (Fedora). All was OK until I hit the pyscenic ctx command. My command is below:
`pyscenic ctx \
./expr_mat.ad…
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Hi scFunctions Developer,
Nice package for doing this.
But in the tutorial, I think you missed the code for calculating the RSS.
Nevertheless, I got an error while I tried to do that:
rrs_df
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Hi,
Thank you very much for the wonderful tool. I would like to create module lists for iRegulon analysis. However, I'm getting an error message during the module pick-up step. Could you please hel…
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when I run the following codes:
> pyscenic ctx --num_workers 10 \
> --output sce.regulons.csv \
> --expression_mtx_fname sce.loom \
> --all_modules \
> --mask_dropouts \
> --mode "dask_m…
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Hi,
Thank you for developing SCENIC.
I'm a new user of pyscenic. When I tried to rerun the case study "GSE103322 - Head and Neck Squamous Cell Carcinoma (HNSC)", an unexpected problem occured.
Wh…
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Hi
First of all, thank you so much for this excellent tool and straightforward tutorials to follow.
I have one question. When I am trying `pyscenic ctx` CLI module with default parameters (which…
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**Describe the bug**
Following the "Tutorial: Branched differentiation trajectory" I tried to create an UMAP from the eRegulon AUC but the output is just a mix of all the celltypes. In my understandi…