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Dear developers,
What is the optimal format for Dorothea (bulk transcriptome analysis)? Is this FPKM, normalised counts, log normalised counts??
In the modern annotations, we have up to 50000 gen…
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I'm working on analyzing a large number of single-cell datasets and would like to add regulon analysis. Initially I was looking at the R implementation of SCENIC, but would rather use pySCENIC; I've g…
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Dear Julio,
Do you have a script on how to combine regulon data from OmniPathR with the BioConductor package “viper”?
Much appreciated. Thanks.
Steven Van Laere
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Hello,
Thanks for the great work on pySCENIC! been using R version and pySCENIC is so much faster!
Though, I can't seem to find some feature (eg. TSNE, histogram plots) for regulons' expressio…
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Hi,
I am interested in identifying TF regulons that might be different across cell types ( the pyscenic tutorials show this) , but also across conditions in each cell type. So i wondered what was t…
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Hi,
I have a huge single-cell dataset (>600k cells) from different animals and different conditions/timepoints. After filtering, I have ~15k genes to work with.
Although I work on a HPC, but a…
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Hi,
I am trying to run export2loom so that I can view the results of my command line pySCENIC analysis in SCope.
I have three questions:
1. Why does it not like regulon names similar to the f…
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I get this error. It seems to be looking for something that's not there.
> dorothea_regulon_human str(dorothea_regulon_human)
tibble [486,751 × 4] (S3: tbl_df/tbl/data.frame)
$ tf : chr …
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Hi,
I'm trying to open a loom file that is the output of pySCENIC, and I'm getting this error:
```
> loom
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Hi,
I have followed the [tutorial](https://pyscenic.readthedocs.io/en/latest/tutorial.html) for pySCENIC and am now implementing the [scenic protocol](http://htmlpreview.github.io/?https://github.co…