Seppe De Winter comments

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                                            Seppe De Winter

scenicplus prepare_data prepare_menr error

Hi @Yiming-Huang-neuron One or more of your cistromes seems to be empty ... Can you check wether this is the case? All the best, Seppe

scenicplus prepare_data prepare_menr error

@Yiming-Huang-neuron Could you share the entire stack trace + command you were running so we can help troubleshooting further? All the best, Seppe

Problem with TSS

Hi @ReviewBrandLab2024 This looks like a lot of errors, can you run ```bash pycistopic tss gene_annotation_list ``` in a bash (zsh, ... not python) kernel and show the output please?...

کتابخانه نصب نمیشه یک ماهه تلاش میکنم حتی در محیط مجازی کوندا نیز نصب نمیشه

Hi @sajadfatahi Could you please detail your issue? All the best, Seppe

How to run SCENIC+ with Signac processed data

Hi @zhli12 and @mluciarr You can still find this tutorial here: https://github.com/aertslab/pycisTopic/blob/old/notebooks/Toy_melanoma-RTD.ipynb All the best, Seppe

TypeError: score_eRegulons() got an unexpected keyword argument 'scplus_obj'

Hi @LukasOussoren Thank you for opening this issue! Yes, I missed this while updating the code, I did not realise this ... Added to my todo list! Best, Seppe

TypeError: score_eRegulons() got an unexpected keyword argument 'scplus_obj'

Hi @LukasOussoren This code has now been updated: https://scenicplus.readthedocs.io/en/latest/Perturbation_simulation.html#Tutorial:-Perturbation-simulation All the best, Seppe

pyscenic dependency

Hi @wangjiawen2013 SCENIC+ is a separate package, it does have pyscenic as a dependency though. All the best, Seppe

pycisTopic find_diff_features function stopping abruptly at Starting a local Ray instance

Hi @ptk1601 Can you check if you are running out of memory perhaps? @ghuls has also been updating this code. It should run much smoother with his new version. Best,...

Different batches/studies

Hi @Flu09 I would suggest to run it on the concatenated matrix. Best, Seppe