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Details of datasets #24

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raman91 opened this issue Sep 4, 2024 · 1 comment

raman91 commented Sep 4, 2024

Hi,

Thank you for developing this great tool. May i know in detail what files should be present for CosMx, stereo-seq data?

Collaborator

xhelenfu commented Sep 4, 2024

Hi, the files under files in the .yaml file are needed for each dataset. Please refer to https://github.com/SydneyBioX/BIDCell/blob/main/bidcell/example_params/cosmx.yaml and https://github.com/SydneyBioX/BIDCell/blob/main/bidcell/example_params/stereoseq.yaml as examples. Please note that for stereo-seq, fp_selected_genes is also needed, which contains a list of the selected genes to use (typicallly HVGs).

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