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jsxlei / SCALE

Single-cell ATAC-seq analysis via Latent feature Extraction
MIT License
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input dimension #19

Open hongruhu opened 2 years ago

hongruhu commented 2 years ago

Hi, I was wondering for your original publication, how large the input dimension (number of peaks) the SCALE model can accommodate. Sometimes the scATACseq give us over 100k features/peaks, I was curious about that if you included all the peaks from the scATACseq data or just selected those highly variable peaks. Thanks

jsxlei commented 2 years ago

Hi, SCALE model can accommodate over 100k features/peaks, though the default for the current version is select 30,000 highly variable peaks. To include the all the peaks, just git clone the latest code in the github, and use option --n_feature = -1 and --min_cells 0. If you have any other questions please let me know.

hongruhu commented 2 years ago

Thanks.