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...
Hello, I am trying to run the grn step on a large dataset of 263159 cells and 14357 genes on an HPC cluster with 999 GB of memory and 16...
I ran the GrnBoost2 algorithm on my bulk transcriptomics data and now want to predict regulon using cisTarget. My code raised "could not convert string to float: " error. ADJACENCIES_FNAME...
With R I had many TF and targets with importance levels above 200 when running the Genie3 step However, I when running almost the same dataset with pyscenic using the...
Hi , I have an issue and could not find the solution in the documentation. When I run CTX it kills the process early on, because it thinks the workers...
Hello, I was encountering dask issues while running pyscenic grn, and so I switched over to using arboreto_with_multiprocessing.py as suggested in previous posts. However, I am running into an error...
Hello, I am using CLI to run the pyscenic. and it seems it has been installed properly. I wanted to run the grn for a big dataset (17627, 23657) and...
Dear pyscenic development team, I encountered some problems when using “pyscenic ctx” **Describe the bug** > "mm9-500bp-upstream-10species.mc9nr.genes_vs_motifs.rankings.feather" is not a cisTarget Feather database in Feather v1 or v2 format. when...
Hi, When I run clustering with sns.clustermap(), an error occurred: FloatingPointError: NaN dissimilarity value. It caused by an weired value in the auc matrix. Some regulons (such as Ppp2r3d(+)) auc...
Hello, I had question in regard to the updated databases for the latest release. I see that the feather v2 files are now available on cisTarget databases. However, what about...
I analyze according to the standard tutorial, but there are always errors. This is my running log. I hope to get your reply Thanks! pyscenic ctx adj.sample.tsv $f_db_names --annotations_fname motifs-v10nr_clust-nr.hgnc-m0.001-o0.0.tbl...
