SCENICprotocol
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aertslab
A scalable SCENIC workflow for single-cell gene regulatory network analysis
I get the following error while trying to run AUCell step from the tutorial (http://htmlpreview.github.io/?https://github.com/aertslab/SCENICprotocol/blob/master/notebooks/PBMC10k_SCENIC-protocol-CLI.html) /home/xx/.local/bin/pyscenic aucell filtered_scenic.loom reg.csv --output pyscenic_output.loom --num_workers 4 2023-05-03 15:40:13,037 - pyscenic.cli.pyscenic - INFO -...
(base) [ahmu@AMD demo]$ nextflow run aertslab/SCENICprotocol -profile singularity --loom_input /home/ahmu/demo/CS78-EPI5718.loom --loom_output pyscenic_integrated-output.loom --TFs /home/soft/scenicDB/allTFs_hg38.txt --motifs /home/soft/scenicDB/motifs-v9-nr.hgnc-m0.001-o0.0.tbl --db "/home/soft/scenicDB/hg38/*feather" --pyscenic_container=/home/soft/aertslab-pyscenic-scanpy-0.12.1-1.9.1.sif --seed 777 N E X T F L O W ~...
Hello, there is something wrong when I import the package, and I found that there is no function called "scatterplots" in the .py file. Could you help me deal with...
When I load the f_final_loom into a `scanpy.AnnData` object, I get the following error. `adata.obs.drop(['Embedding','Embeddings_X','Embeddings_Y','RegulonsAUC'],axis=1,inplace=True)` TypeError: void() takes exactly 1 positional argument (0 given) And the content of obs: obs:...
Hi, I would like to run PyScenic on a 10X dataset of 195,000 cells we have generated from mouse bone marrow. The dataset is overall quite diverse in terms of...
Hello, I'm currently running the Docker version of pyscenic (0.12.1) on HPC (Fedora). All was OK until I hit the pyscenic ctx command. My command is below: `pyscenic ctx \...
Hi team, Would you please suggest what cause the kernal dead error? Thank you so much! This cell ran for about 2 hours and then I got the error kernal...
Dear SCENIC team, I am following the SCENIC tutorial on processing the PBMC 10K data and I have generated the final pbmc10k_scenic_integrated-output.loom file. However, I could not load this loom...
I am running the PBMC10k_SCENIC-protocol-CLI.ipynb file from the tutorial on the website, and I am getting an error at this step: `import json` `import zlib` `import base64` `# collect SCENIC...
I am running pySCENIC in command line via docker. I have run the three Docker steps: docker run -it --rm \ -v /data:/data \ aertslab/pyscenic:0.12.0 pyscenic grn \ --num_workers 6...
