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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,
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 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,
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…
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Hi,
What is the easiest way to save the modules/regulons generated by pyscenic as a txt file? Eventually, I would like to export them in some way so i can read them into R.
thank you!
Joe
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Hi Everyone,
I am using pypath 0.8.18 with Python3.6 on Ubuntu 18.04.
I tried to load annotation from pypath.annot.AnnotationTable() and get following error message:
File "/usr/lib/python3.6/z…
luli7 updated
5 years ago
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I found in the [preprint](https://www.biorxiv.org/content/biorxiv/early/2018/11/28/479857.full.pdf) that "All regulon datasets, random regulons, GENSOR Units, custom scripts and the raw data used in t…