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I'm trying to use the function run_viper to calculate transcription factor activity based on an earlier differential expression analysis I ran but running the following line:
tf_activities_stat
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Dear SCENIC team,
Thanks for the great tool SCENIC!
I have encountered an error when i try to analyze my 10X genomics scRNAseq data followed the instruction "https://github.com/aertslab/SCENICprotoc…
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Hi! I found your finding very interesting. I wonder if you can provide modules.RData for modules. I was trying to go over the whole process to get the cell state values.
Thank you!
Peiyao
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Can any one help me with a hint why I cannot read fully in output from pySCENIC in to Rstudio? I used pyCENIC to run the SCENIC workflow and I used the following command
`
(base) charles@rahul-SYS…
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Dear team
I keep getting the error below in the last step of pyscenic pipeline. I found it was raised before but the solutions suggested didn't work. There seem to be some incompatibility in the …
Sa753 updated
3 months ago
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Hello,
I am using CollecTRI to study mouse genome, when I run in R `net
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Hi, I have questions about how to carry out pySCENIC analysis correctly using data from more than a single sample. For example, I am working with data from 3 biological replicates which I intend to in…
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Hello pyscenic,
For the heatmap (coding below), is it possible to sort it by cell type colors? I mean the cells from the same cell types aggregate together to make the color bar in an ordered patte…
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Hi,
I was wondering whether you have compared the success of pySCENIC analysis at identifying "true" gene modules downstream of different normalisation methods. In particular, I am interested in…
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Hi, I run the following function on my date:
from scenicplus.loom import *
export_to_loom(scplus_obj,
signature_key = 'Gene_based',
tree_structure = ('Patient 1', …