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...
Hi @cflerin , There are two outputs in the standard pipeline. 1) Adjacencies based on GRN. Here we see an 'importance' score for each target gene and Transcription factor relationship....
Hi, I am currently using SCENIC to identify some clusters and explore others in my data. I was wondering how to ask the right questions which could allow me to...
Hi guys, I want to start using pySCENIC on my virtual environment, where I am using miniconda to create the virtualenv and install packages. As a rule, I like to...
[results] Is there a way to control the parallel computing in python script instead of CLI version?
Hey, I am wondering if there is a way to specify the core for the python function when running the function. I checked the arboreto package but it seems like...
**Describe the bug** Error when running pyscenic grn. I am using an older version of dask (1.0.0) as previously suggested. **Steps to reproduce the behavior** 1. Command run when the...
Hi, Thank you for developing this great tool. And I need a little instruction in maybe the final step , after nearly a month of struggling, I finally got the...
Hi - Recently, I am running pySCENIC on Rat. As for the MOTIF_ANNOTATIONS file, I replace the genes in “motifs-v9-nr.mgi-m0.001-o0.0.tbl” with Rat's genes, but the process was broken like the...
Hi team, Thank you for providing a great tool. Could you please explain more details of how to generate a zebrafish motif annotation database (Motif2TF format)? Or even it would...
Hello, In order to explore the regulons identified in my data with pySCENIC, I used the list of target genes for select regulons and analyzed them using iRegulon. However, after...
Hi. I run the pySCENIC CLI and get 3 csv files. `expr_mat.adjacencies.tsv` from Step 1 `grn` `regulons.csv` from Step 2 `ctx` `auc_mtx.csv` from Step 3 `aucell` After inspecting the regulon...
