anke-king

Thank your for your reply! Just for clarification: I have one data set with cell types for training and a second data set with cell typest which are not in...

Okay, in case anyone else has this problem and after hours of trying everything I finally found a solution on how to fix this for me: install gcc with home-brew...

I did everything exactly like you said and still get this error: running install running build running build_py running build_ext cythoning DP_GP/core.pyx to DP_GP/core.c Error compiling Cython file: ------------------------------------------------------------ ......

I did install gcc via Conda and I still get the same error when running setup.py

I used the default, so not specifying anything (trying to follow your tutorial) Here is a short subset of my var_names: print(adata_human_mouse.var_names[adata_human_mouse.var_names.str.startswith("CCL")]): Index(['CCL1', 'CCL11', 'CCL12', 'CCL15', 'CCL15-CCL14', 'CCL17', 'CCL22', 'CCL23',...

Hi, thanks for your reply. I checked, and I don't have nans or zeros.

I do have negative values, as the data is normalized, scaled and transformed. Does your tool need raw data? Because in the tutorial you also do standard preprocessing steps.

thanks for your help! I changed my code and now use log transformed values (so no nan, no negative) instead of scaled, however I still get the same error.

I even tried adding 1e-6 to each value and only using highly variable genes because I thought maybe somewhere the algorithms divides by zero, but the float division by zero...

How do I pass the database if I have installed it via bash INSTALL.sh $KmerFinder_DB viral? when I pass the path to my directory I installed it in I get...