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wanglab-broad / ClusterMap

ClusterMap for multi-scale clustering analysis of spatial gene expression
GNU General Public License v3.0
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Vignette Enhancement #2

Closed rocketeer1998 closed 2 years ago

rocketeer1998 commented 2 years ago

Hi @heihaizhengdong Thanks for your excellent work! And I'd like to use clustermap to analyze my ISS data. However, I'm totally a beginner in python. So could you provide a more detailed vignette on the module installation, and a test run using test data? Thanks!

yichunher commented 2 years ago

Hi, Thanks for asking! For installation please refer to the post here: https://github.com/wanglab-broad/ClusterMap/issues/1#issuecomment-999330366 For test run on test data, please refer to two jupyter notebooks here and here.

rocketeer1998 commented 2 years ago

Hi, Thanks for asking! For installation please refer to the post here: #1 (comment) For test run on test data, please refer to two jupyter notebooks here and here.

OK. Thank you! I'll give it a try and go back to you later.

rocketeer1998 commented 2 years ago

Hi @heihaizhengdong , I'm installing ClusterMap on my Windows10 computer following your instruction. But I got a long list of ResolvePackageNotFound error after typing conda env create -f environment.yml. I've tried to solve this problem by moving the problematic dependencies from dependencies to pip in environment.yml file. So the environment is successfully created. However, I still can't import the modules that i need in Clustermap. Any recommendations?

rocketeer1998 commented 2 years ago

Hi @heihaizhengdong , I'm installing ClusterMap on my Windows10 computer following your instruction. But I got a long list of ResolvePackageNotFound error after typing conda env create -f environment.yml. I've tried to solve this problem by moving the problematic dependencies from dependencies to pip in environment.yml file. So the environment is successfully created. However, I still can't import the modules that i need in Clustermap. Any recommendations?

Solved it for now. And I can import all the modules included in STARmap_human_cardiac_organoid vignette correctly. But I didn't create a new environment in the way which is illustrated above because there were so many "packages conflicts".

yichunher commented 2 years ago

Hi,

Sorry for the late reply. Glad to see the problem was solved!