Chris Doan

Hi @SeppeDeWinter, it is 3.6.0. Thank you! ``` import matplotlib matplotlib.__version__ ``` Would you please have a look at this error which is more important? https://github.com/aertslab/scenicplus/issues/252

Hi @JuanruMaryGuo. Have you run this cell? I have an error. ``` from scenicplus.wrappers.run_pycistarget import run_pycistarget run_pycistarget( region_sets = region_sets, species = 'homo_sapiens', save_path = os.path.join(work_dir, 'motifs'), ctx_db_path = rankings_db,...

Hi @SeppeDeWinter The kernel dying at this cell: ``` from scenicplus.wrappers.run_pycistarget import run_pycistarget run_pycistarget( region_sets = region_sets, species = 'homo_sapiens', save_path = os.path.join(work_dir, 'motifs'), ctx_db_path = rankings_db, dem_db_path = scores_db,...

Hi @SeppeDeWinter, sure. That function printed a lot of output during about 2 hours of running: 2023-11-14 14:33:44,142 pycisTarget_wrapper INFO pbmc_tutorial/motifs folder already exists. 2023-11-14 14:33:45,422 pycisTarget_wrapper INFO Loading cisTarget...

Hi @SeppeDeWinter, Thank you for your suggestion. I put 1024Gb in memory, so may I know how much memory we need to run?

Hi @SeppeDeWinter This is what I have in the end of the log file: ``` [I 16:02:55.296 NotebookApp] Saving file at /project/multiome.ipynb [I 16:16:57.060 NotebookApp] KernelRestarter: restarting kernel (1/5), keep...

Hi @ghuls, the file name I download were a little different with the file name in the tutorial which caused the error. Thank you so much! However, I ran into...

Thank you! `conda install -c anaconda graphviz` returned no error, however: `pip install pygraphviz leidenalg scanpy cello-classify` #include "graphviz/cgraph.h" ^ compilation terminated. error: command '/usr/lib64/ccache/gcc' failed with exit code 1...

Thank you! It worked! `model_prefix = 'GSM3516673_MSK_LX682_NORMAL′` File "", line 1 model_prefix = 'GSM3516673_MSK_LX682_NORMAL′ ^ SyntaxError: EOL while scanning string literal Would you please tell me how to fix this?...

Hi, I installed cello on a server, so it is different from a local computer when open Jupiter notebook. When I copied and pasted the URL as the instruction, I...