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Apologies if this is a naive question, but if different PWM reflect the extent of the promoter sequence considered for possible TF targets, would that make a `500bp_up_and_100bp_down_tss` PWM a su…
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Hello,
I've read your recent Nature Methods paper with great interest. Our lab studies transcriptional networks, and I am currently trying to apply it to my single-cell data set.
Thanks for the …
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when run
%time
auc_mtx = aucell(exp_mtx, regulons, num_workers=32)
auc_mtx.to_csv(AUCELL_MTX_FNAME)
error
CPU times: user 13 µs, sys: 1 µs, total: 14 µs
Wall time: 26.2 µs
------------…
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Hi There,
TCGA regulons are not accessible. Please help.
Code:
data(dorothea_hs_pancancer, package = "dorothea")
Warning message:
In data(dorothea_hs_pancancer, package = "dorothea") :
data …
boseb updated
3 years ago
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**Describe the bug**
I am able to get csv output from `pyscenic aucell` but it throws an error when it tries to write to the output loom file using `h5py.h5d.create`. The following command does crea…
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Hi!
I've seen a couple threads (#136 #157) that mention running the pySCENIC pipeline multiple times and then aggregating the regulons across runs.
My current approach to this has been to take t…
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Hi,
I got the following errors when running the functions for building and scoring the GRN:
```
> scenicOptions = runSCENIC_1_coexNetwork2modules(scenicOptions)
08:29 Creating TF modules
Numb…
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Hi,
Unfortunately I can't get pySCENIC to work in Python, so I have been using the command line tool.
I have two questions:
1. I have three output files from the command line version - "mer…
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I loaded the regulon network from the [dorothea package](https://github.com/saezlab/dorothea/blob/master/vignettes/single_cell_vignette.Rmd):
```
## We read Dorothea Regulons for Human
dorothea_r…
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https://mp.weixin.qq.com/s/-jAaHAvraGnVLsPLGKTvQA
ixxmu updated
2 years ago