pySCENIC
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aertslab
pySCENIC is a lightning-fast python implementation of the SCENIC pipeline (Single-Cell rEgulatory Network Inference and Clustering) which enables biologists to infer transcription factors, gene regula...
**Describe the bug** Process `filter` terminated with an error exit status **Steps to reproduce the behavior** 1. Command run when the error occurred: ```python nextflow run aertslab/SCENICprotocol -profile docker ```...
Hello, so I managed to get until the Phase II of your Tutorial with your data. But after running 145h I stopped the process. I don't know if it is...
Hi, How to generate binary heatmap used in your nature protocol paper (A scalable SCENIC workflow for single-cell gene regulatory network analysis, Fig.13)? It seems that it cannot be generated...
Hi all, Sorry if this has been asked before; SCENIC seems like really cool technology but I am having trouble interpreting the results. What does relaxing the NES criterion to...
Hello! Happy Holidays, and I hope you are doing well. I am currently using PySCENIC to run some analyses for a Sea Urchin scRNA Dataset. However, there doesn't seem to...
Hi, how to use binarization.py in jupyter notebook and shell ? I ran auc_mtx_binary = binarize(auc_mtx,num_workers=15) in jupyter notebook Some warnings and errors occured: /home/wangjw/bin/miniconda3/envs/scenic/lib/python3.6/site-packages/pyscenic/diptest.py:30: RuntimeWarning: divide by zero encountered...
I have a doubt on how to properly use pySCENIC and iRegulon. I am comparing two conditions, Case and Control, and I want to test two possible analyses: - Differential...
I'm curious to know if it would make sense to do something like this. The example is that all the steps needed to generate a regulon.p file were performed on...
Many SCENIC jobs are very long running and a user can wonder if progress is being made. Having a mechanism to track progress would be very useful.
Thanks for your software! I found that the final result of pyscenic is not the same as the result of scenic. In the result of scenci, the activity of each...
