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, So I'm not sure if this is a bug or not. However when I run GRN on a large dataset, GRN completes the infer partial partitions, then restarts and...
Hi, I finished grn -> ctx -> aucell analysis and have an output loom file which I am able to visualize on scope. But I am trying to combine this...
Hi, I got a bug when I want to create the modules for iRegulons. here is my error : Can you help me? Thank you, Steven
Hi First of all, thank you so much for this excellent tool and straightforward tutorials to follow. I have one question. When I am trying `pyscenic ctx` CLI module with...
when run `sc.utils.sanitize_anndata(adata)`, it returns: `AttributeError: module 'scanpy' has no attribute 'utils'` I didn't find any information about sanitize_anndata under the path of scanpy, does anyone encounter a similar error?...
I ran the complete pySCENIC pipeline and ranked the importance of the regulons with the RSS function per subtype of macrophages (roughly 12 different subtypes). It occurs often, however, that...
I am running nextflow DSL2 multiruns and first testing it on a small no of runs 2 to see if it is working on a few runs before doing a...
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...
Hi, Following this protocol [here](https://github.com/aertslab/SCENICprotocol) to run pyscenic on the test pbmc dataset but its failing with this error `nextflow run aertslab/SCENICprotocol \ -profile docker,test` ``` > -profile docker,test CAPSULE:...
Hello, So I have uploaded all the appropriate files needed to run pyscenic (TF list, motif, expression file, etc.) but I am still getting an error when I run the...
