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...
I've been seeing my `pyscenic ctx` gets terminated in the middle of the run. My mystery is that it doesn't throw any error message as shown below: ```bash $ singularity...
**Describe the bug** A clear and concise description of what the bug is. I am encountering a very wired problem about running the pyscenic on a HPC, on which the...
**Hello Scenic developers, I wanted to express my gratitude for creating such an amazing tool. I've used SCENIC to analyze single-cell data that we're interested in incorporating into our Nextflow...
Error running: pyscenic grn \ --num_workers 20 \ --output adj.tsv \ --method grnboost2 \ PBMC10k_filtered.loom \ hs_hgnc_tfs.txt ``` (...) distributed.worker - WARNING - Memory use is high but worker has...
I am currently using pyscenic ctx for analysis, but I encountered the following error: ```python Traceback (most recent call last): File "/home/qiruicheng/anaconda3/envs/scenic_protocol/bin/pyscenic", line 8, in sys.exit(main()) File "/home/qiruicheng/anaconda3/envs/scenic_protocol/lib/python3.6/site-packages/pyscenic/cli/pyscenic.py", line 675,...
I got thousands of these warnings when I run pyscenic ctx on linux (ubuntu 22.04) CLI (conda environment): `pyscenic.transform - WARNING - Less than 80% of the genes in some_gene...
Hi, thank you for the great tool! I have managed to run the inital steps of the workflow but am not able to run aucell as the job is killed...
Hi, I failed to run grnboost2 on a large dataset with shape 50000 cells X 28000 genes. Then I subsample the dataset to a small one and run grnboost2 sucessfully....
**Describe the bug** the datatype of the dataframe object generated by prune2df may be wrong **Steps to reproduce the behavior** 1. Command run when the error occurred: ``` df =...
**Describe the bug** Package doesnt have this modle ModuleNotFoundError: No module named 'pyscenic.rnkdb'
