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ChuanXu1 avatar ChuanXu1 commented on June 16, 2024

@pcm32, you can provide a symbol-to-ID mapping file (one column being gene symbols and the other column being IDs), and use it to convert the model from gene symbols to Ensembl IDs.

#load a model
model = celltypist.Model.load("some_model.pkl")
#convert the model
model.convert("path_to_your_mapping_file")
#prediction
predictions = celltypist.annotate(input_data, model = model)

In the new version (1.6.1), I also added a mapping file based on GENCODE version 44. So you can use it if you do not find a mapping file yourself. Details can be found in the online tutorial (https://github.com/Teichlab/celltypist -> Usage (classification) -> Supplemental guidance -> Model conversion from gene symbols to Ensembl IDs)

from celltypist.

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