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Hi!
I am interested in some regulons that have 500-1000 gene targets. I'm looking for a way to rank those gene targets based on how good of a potential target it is for the given TF. I use the CLI …
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I followed the tutorial page https://pyscenic.readthedocs.io/en/latest/tutorial.html to try to run pySCENIC, but during importing there is already an error.
```
import os
import glob
import pick…
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I have been using pySCENIC on a few datasets locally but have been looking into larger datasets that required me to move to an HPC infrastructure.
My dataset is not huge, around 10k cells and 17k gen…
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Hi Florian
In the example "complete pipeline", there is a little problem with the dataset: the default value for the calculate_rrs function will not be found, and no value is actually set.
Just mo…
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Hi @cflerin @bramvds @ghuls,
I generated a ```regulons.csv``` file as output of the CLI ```pyscenic ctx```. What would be the easiest way to import this file into the scanpy pipeline as to use the …
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Hello,
I am getting this error the running modules = list(modules_from_adjacencies(adjacencies, ex_matrix)) :
2020-03-23 13:46:47,461 - pyscenic.utils - INFO - Calculating Pearson correlations…
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Dear team. Great tutorial and package!
When I create the regulon heatmaps, is there a way to add my previously determined identities of each cell?
I didn't understand my way around the "cellInfo" an…
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Update the following URL to point to the GitHub repository of
the package you wish to submit to _Bioconductor_
- Repository: https://github.com/saezlab/dorothea
Confirm the following by editing…
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Hi,
I'm trying to run the pyscenic CLI, I have already managed to run the grn step and I got an output "adjacencies.tsv", but when I proceed to the ctx step I have a KeyError.
My command is the foll…
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Hi!
Some of the functions (specially regards to metadata) do not work with v3 loom files. I have also opened an issue in the loomR GitHub. Meanwhile, could some functions be added for dealing with …