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The early steps of Scenic appear to have worked well on my dataset of ~350 cells, using a server session with access to 50GB RAM. However, the following error appeared >12 hours into running the runSC…
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Hi Loom team,
I am having trouble reading in a loom file using loompy. I started a jupyter lab session in a conda environment and tried to read in a loom file from http://scope.aertslab.org/#/Bernard…
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I am getting the following error when I run runSCENIC_3_scoreCells, could you please tell me how to fix it.
runSCENIC_3_scoreCells(scenicOptions, exprMat_filtered)
22:36 Step 3. Analyzing the ne…
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This ticket #14892 will lead to a lot of changes, so I am trying to split up some sub-issues.
Merge 'GO:0015683 ferric iron transmembrane transport'
into
'GO:0098706 ferric iron import across pl…
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Hello,
I am implementing pyscenic on my laptop (MacPro 2.6 GHz Intel Core i7) using the command as followed:
`pyscenic grnboost -o scenic_out/grn_output.tsv @grn_args.txt`
in which grn_args.txt …
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Hi there!
So excited to see all of this incredible work ported into Python! The performance in our hands has moved things from about a day-long computation to somewhere around half an hour—so thank…
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sorry to keep bombarding you!
```
>>> sns.clustermap(auc_mtx, figsize=(8,8))
Traceback (most recent call last):
File "/usr/local/lib/python3.6/site-packages/scipy/cluster/hierarchy.py", line 2…
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Regulons don't use CPM or log normalisations and don't need to be redrawn
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Add function for retrieving markers from gene sets, clusters and regulons.
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extend getCellColorByFeatures by new arguments:
>coordinatesID
>ageingAnnotationID
add possibility to put clusters next to genes and regulons