I have considered a way to compute a gene expression correlation coefficient in a spatial context and it was lucky for me to find this method (copulacci). Our lab reviewed the bioinformatics paper recently published and it was very interesting! I am considering applying the copulaci to 10x Visium HD data. I am also wondering if the method can handle such high-resolution data in a reasonable computational resource and time. I couldn't find any performance evaluation in the manuscript. Thank you!
*** I followed the installation instructions. I created a conda environment w/ python=3.9, git clone, and run setup. I got this error message and the installation failed with the following error message. Is there any installation requirement? I searched Google w/ the error message but I have no clue.
Collecting urllib3[socks]<3,>=1.26 (from selenium->spatialdm->copulacci==0.0.1)
Using cached urllib3-2.2.1-py3-none-any.whl.metadata (6.4 kB)
Using cached urllib3-2.2.0-py3-none-any.whl.metadata (6.4 kB)
Using cached urllib3-2.1.0-py3-none-any.whl.metadata (6.4 kB)
Using cached urllib3-2.0.7-py3-none-any.whl.metadata (6.6 kB)
Using cached urllib3-2.0.6-py3-none-any.whl.metadata (6.6 kB)
Using cached urllib3-2.0.5-py3-none-any.whl.metadata (6.6 kB)
Using cached urllib3-2.0.4-py3-none-any.whl.metadata (6.6 kB)
Using cached urllib3-2.0.3-py3-none-any.whl.metadata (6.6 kB)
ERROR: Exception:
Traceback (most recent call last):
File "xxx/miniforge3/envs/copulacci/lib/python3.9/site-packages/pip/_internal/cli/base_command.py", line 180, in exc_logging_wrapper
status = run_func(*args)
File "xxx/miniforge3/envs/copulacci/lib/python3.9/site-packages/pip/_internal/cli/req_command.py", line 245, in wrapper
return func(self, options, args)
File "xxx/miniforge3/envs/copulacci/lib/python3.9/site-packages/pip/_internal/commands/install.py", line 377, in run
requirement_set = resolver.resolve(
File "xxx/miniforge3/envs/copulacci/lib/python3.9/site-packages/pip/_internal/resolution/resolvelib/resolver.py", line 95, in resolve
result = self._result = resolver.resolve(
File "xxx/miniforge3/envs/copulacci/lib/python3.9/site-packages/pip/_vendor/resolvelib/resolvers.py", line 546, in resolve
state = resolution.resolve(requirements, max_rounds=max_rounds)
File "xxx/miniforge3/envs/copulacci/lib/python3.9/site-packages/pip/_vendor/resolvelib/resolvers.py", line 457, in resolve
raise ResolutionTooDeep(max_rounds)
pip._vendor.resolvelib.resolvers.ResolutionTooDeep: 200000
