Modules scanpy_helpers / AnnotationHelper

[bangbattlers]

Hi,

I love to explore these thrilling datasets and code, but I've got one error I want to ask.

From the code at analyses/37_subclustering/37_neutrophil_subclustering.py
I tried to import following modules and functions

"from scanpy_helpers.annotation import AnnotationHelper
import scanpy_helpers as sh"

, but I countered the errors that there is no module scanpy_helpers neither AnnotationHelper.

From Googling, I seems there are no module called scanpy_helpers neither AnnotationHelper that I can install.
How could I use the modules ? Is there any specific routes that I can install these?

Thanks
bangbattlers

[Gregor Sturm]

Hi,

the package is in this repo in the lib subfolder. It's not an official package but rather a bunch of customized code for this project.

You can install it like this:

git clone https://github.com/icbi-lab/luca.git
cd luca/lib
pip install -e ./scanpy_helper_submodule