Error while running NSForest on a Scanpy object

JCVenterInstitute / NSForest

A machine learning method for the discovery of the minimum marker gene combinations for cell type identification from single-cell RNA sequencing

MIT License

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Error while running NSForest on a Scanpy object #10

Closed siavashmoghadami closed 3 months ago

siavashmoghadami commented 2 years ago

Hi, I have run NSForest V3.0 using "NS_Forest(adata, clusterLabelcolumnHeader = "leiden"" command in Jupyter Notebook (on a Windows 10 OS) and the program ran for a while. However, after a few minutes I got this message:

File :1 6330403 K07Rik >=1.4837858080863953 ^ SyntaxError: invalid syntax

Would you please help me solve this issue?

siavashmoghadami commented 2 years ago

As an update, I realized that NSForest has an issue with gene names starting with numbers such as "6330403K07Rik" or "3110035E14Rik".

yunzhang813 commented 3 months ago

Thanks of the ticket. Code refactored in v4.0.