Seppe De Winter

Hi @josephineyates Thank you for the bug report. This is indeed a mistake in the code. I'll try to fix it soon. Best, Seppe

Hi @mtrebelo Does any of cell type labels contain spaces or special characters? Also I see that `bigwig_path` is set to `'wor_dir'`` instead of `'work_dir'`. Besides these things you can...

Hi @MohammadIzadi Did you try running the code with single cpu core? Best, Seppe

Hi @alexlenail Sorry for the late reply! Trails we have done in the past (while developing SCENIC) have shown that both raw counts and normalised counts work similarly. I would...

Hi @YayanFeng55 I would suggest to use the code in the development branch. See this discussion on how to run it: https://github.com/aertslab/scenicplus/discussions/202 All the best, Seppe

Hi @YangLi-Bio Downgrading your pydantic version to 1.x might solve your issue, see: https://discuss.ray.io/t/pydantic-dataclasses-dataclass-only-supports-init-false/11278. This piece of code can help with debugging: ```python import ray ray.init( num_cpus = 5, _temp_dir...

Hi @YangLi-Bio Sorry to hear that downgrading did not work. Just to be sure, running ```python import ray ray.init( num_cpus = 5, _temp_dir = os.path.join(tmp_dir + 'ray_spill')) ``` does not...

Hi @YangLi-Bio Can you show: ```python cistopic_obj.selected_model.topic_region ``` Best, Seppe

Hi @sid5427 From the error I suspect that `region_sets['DARs']` might be empty or contain empty entries. Could you show the output of `region_sets['DARs']` to confirm this? On your question wether...

Hi @sid5427 Yes indeed, it's these empty dataframes in `markers_dict` that is causing the error (i.e. 'CD14-Mono', 'MPP Ribo-high' and 'MPP SPINK2-CD99'). You should remove this prior to running: ```python...