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bioinfo-ibms-pumc / SCSA

SCSA: cell type annotation for single-cell RNA-seq data
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updated markers? #14

Open ajneville opened 3 years ago

ajneville commented 3 years ago

Hi, I was wondering if the marker database you have (for mouse) has even been updated? I used SCSA about 6 months ago, and am going to be using it now. Is there a reason for me to update the scsa package? Thanks!

bioinfo-ibms-pumc commented 3 years ago

Sorry for delay. I'm sorry that there is no change for the cell marker database since no updating news could be found on the CellMarker website. But some small bugs in SCSA were fixed from other peoples' feedback. Thank you for your attention!

jasonleongbio commented 1 year ago

Hi @bioinfo-ibms-pumc

Thanks for developing this great tool!

As the CellMarker database has been recently updated to version 2.0 (with many more manually curated markers being added to the database; ref. https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkac947/6775381), may I know if you have any plan to update the marker database for SCSA as well? (If not, perhaps I have to manually add the new marker info of cell types of interest from CellMarker 2.0 to my own .db file first...) Thanks so much!

Starlitnightly commented 1 year ago

Hi @bioinfo-ibms-pumc

Thanks for developing this great tool!

As the CellMarker database has been recently updated to version 2.0 (with many more manually curated markers being added to the database; ref. https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkac947/6775381 ), may I know if you have any plan to update the marker database for SCSA as well? (If not, perhaps I have to manually add the new marker info of cell types of interest from CellMarker 2.0 to my own .db file first...) Thanks so much!

Hi @jpiggod

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!"