pySCENIC

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I saw that `modules_from_adjacencies` function must convert expressions into pandas, which is not friendly to big data. It can directly support anndata?

Liripo

Can pySCENIC only run on Linux? Is it possible to use it on Windows?

2

I want to run pySCENIC instead of running SCENIC in R, but it always fails on Windows.

Always-Stude

[BUG] run in pyscenic grn

2

**Describe the bug** When I run pySCENIC, I often encounter disturbing warnings. I checked the problem may be associated with me this question. https://github.com/aertslab/pySCENIC/issues/482 But I'm not using port 8787....

zhangdong360

TypeError("Must supply at least one delayed object")

1

I used pmbc to test pyscenic, but I had this problem while running the grn step, however I followed the given steps exactly and I am sure my file is...

lpalvin

[ERROR] in running Pyscenic GRN grnboost2

1

**Describe the bug** I am trying to run Pyscenic GRN but its giving me error and i am unable to solve the issue. **Steps to reproduce the behavior** 1. Command...

husain223

[BUG]concurrent.futures.process.BrokenProcessPool: A process in the process pool was terminated abruy while the future was running or pending.

1

when I run the following codes: > pyscenic ctx --num_workers 10 \ > --output sce.regulons.csv \ > --expression_mtx_fname sce.loom \ > --all_modules \ > --mask_dropouts \ > --mode "dask_multiprocessing" \...

YOUWEIQINGHUAN

ctx pyscenic Error

1

Hi, I am trying to compute the Cistarget step of pyscenic after obtaining meta cells with the metacell2 pipeline and then the GRN with arboreta package and saved in a...

angelica-varesi

prune2df fails with TypeError: object of type 'generator' has no len() [BUG]

2

**Describe the bug** I am following the description of the full interactive pipeline as detailed [in this notebook](https://github.com/aertslab/pySCENIC/blob/master/notebooks/pySCENIC%20-%20Full%20pipeline.ipynb) and having trouble running the pruning stage. Using pySCENIC v0.12.1 (installed from...

dmalzl

Expression matrix should be provided in the loom file format.[BUG]

1

hello, **Describe the bug** My shell: ``` pyscenic aucell \ scenic.loom \ reg.csv \ --output pyscenic_output.loom \ --num_workers 5 ``` My log ``` 2024-06-13 13:14:58,995 - pyscenic.cli.pyscenic - INFO -...

bitcometz

When trying to input a pickle (dat) file of regulons for `pyscenic aucell`, I got the following error: `pyscenic.cli.pyscenic - ERROR - binary mode doesn't take an encoding argument`. This...

ggruenhagen3