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bioinfo-ibms-pumc / SCSA

SCSA: cell type annotation for single-cell RNA-seq data
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Request an update of whole.db #28

Closed myshu2017-03-14 closed 1 year ago

myshu2017-03-14 commented 1 year ago

Hi, CellMarker database has been updated to version 2.0 recently.（http://bio-bigdata.hrbmu.edu.cn/CellMarker ） I hope you can update it synchronously.

Best wishes,

Myshu

jasonleongbio commented 1 year ago

Hi @myshu2017-03-14

The request has been proposed in another issue #14 but the authors have not responded yet.

Starlitnightly commented 1 year ago

Hi @myshu2017-03-14

I recently encountered the same issue with the update of whole.db in SCSA package. After working on a solution, I developed a new package called Pyomic which solves this problem. The tutorial of pySCSA can be found at here.

In Pyomic:

Pyomic is now available and I invite you to try it out and provide feedback. You can find more information and installation instructions on Pyomic. I hope this will be helpful for anyone who has faced similar issues with SCSA. Let me know if you have any questions or feedback. Thanks!"

bioinfo-ibms-pumc commented 1 year ago

Thans for all your suggestions. I'm sorry for late because of other things. The database was updated and CellMarker v2 was intergrated. Users can use it with the cmd ' -d whold_v2.db' instead. Thanks again.

myshu2017-03-14 commented 1 year ago

Thans for all your suggestions. I'm sorry for late because of other things. The database was updated and CellMarker v2 was intergrated. Users can use it with the cmd ' -d whold_v2.db' instead. Thanks again.

Hi @bioinfo-ibms-pumc , I recently tested the v2 version of the whole_v2.db and got errors as follow: image

And I also tested the old version only -d parameter was changed, and it ran without errors. Could you help me see how to solve the errors of the new version?

Best wishes,

Myshu

Starlitnightly commented 1 year ago

Thans for all your suggestions. I'm sorry for late because of other things. The database was updated and CellMarker v2 was intergrated. Users can use it with the cmd ' -d whold_v2.db' instead. Thanks again.

Hi @bioinfo-ibms-pumc , I recently tested the v2 version of the whole_v2.db and got errors as follow: image

And I also tested the old version only -d parameter was changed, and it ran without errors. Could you help me see how to solve the errors of the new version?

Best wishes,

Myshu

Hi,

I think you need to change the version of Pandas to 1.5.3 to solve. As a general rule, you need to ensure that the pandas version of the build db file is the same as the author for it to work properly.

myshu2017-03-14 commented 1 year ago

Thans for all your suggestions. I'm sorry for late because of other things. The database was updated and CellMarker v2 was intergrated. Users can use it with the cmd ' -d whold_v2.db' instead. Thanks again.

Hi @bioinfo-ibms-pumc , I recently tested the v2 version of the whole_v2.db and got errors as follow: image And I also tested the old version only -d parameter was changed, and it ran without errors. Could you help me see how to solve the errors of the new version? Best wishes, Myshu

Hi,

I think you need to change the version of Pandas to 1.5.3 to solve. As a general rule, you need to ensure that the pandas version of the build db file is the same as the author for it to work properly.

Yes！ I updated the version of pandas and it worked