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Can anyone summarize what are the dependencies and versions critical for successful running of pyscenic. I have tried most of the methods described in the issues section by double checking the databas…
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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 cores. I tried increasing the cores, but it would cause memo…
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Hi
I managed to run create_cistarget_motif_databases.py for zebrafish and it generated three . feather files, `zf.genes_vs_motifs.rankings.feather`, `zf.genes_vs_motifs.scores.feather` and `zf.motifs…
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Hi there. I've been going through the vignettes and I can't seem to figure out how to get scenicOptions to point to the tsv output file from GRNboost (or a data frame of the results after importing it…
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**Describe the bug**
When the program runs to the prune2df step, it will report an error: ArrowInvalid: Not a feather file. I read your previous discussion and thought it was a problem with the integ…
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**Describe the bug**
With the SCENIC workflow and a loom input with non-standard cell and gene attribute names (`CellID`/`Gene`) the workflow fails to complete.
**To Reproduce**
Steps to reprodu…
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Hi, thanks for the great implementation! I'm trying to run `aucell` on 100k cells and 30k genes with some gene sets and always getting memory error (with `num_workers=1`).First, I need to convert the …
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Hello, when I run create_SCENICPLUS_object, I get the following error, how should I solve this problem
code:
```python
> from scenicplus.scenicplus_class import create_SCENICPLUS_object
> import…
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**Describe the bug**
Running GRNBoost2 produces an error at the very last step.
Reproducible with the tutorial (https://pyscenic.readthedocs.io/en/latest/tutorial.html) using the GSE60361_C1-3005…
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Hey All,
I’m one of the developers behind SCope (https://github.com/aertslab/SCope) and we have been leveraging the loom file format for a long time now to store data not only for SCope, but projec…