How to select gene list

GuangyuWangLab2021 / cellDancer

Predict RNA velocity through deep learning

https://guangyuwanglab2021.github.io/cellDancer_website/

BSD 3-Clause "New" or "Revised" License

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How to select gene list #25

Open mabaoweireadingene opened 7 months ago

mabaoweireadingene commented 7 months ago

Hi Doc ex： gene_list=['Smarca2', 'Rbms2', 'Myo1b', 'Hba-x', 'Yipf5', 'Skap1', 'Smim1', 'Nfkb1', 'Sulf2', 'Blvrb', 'Hbb-y', 'Coro2b', 'Yipf5', 'Phc2', 'Mllt3']

loss_df, cellDancer_df=cd.velocity(cell_type_u_s,\ gene_list=gene_list,\ permutation_ratio=0.125,\ n_jobs=8)

I don't know how to selsect gene_list for my analysis， could you give some advises？ Thanks

Abclisy commented 5 months ago

Hello,

Thank you for reaching out. The preprocessing example allows you to obtain the top 2000 genes. You can also specify your top n genes.

For finding genes of interest, this issue might be helpful.

Best, Shengyu