Request for non-SCANVI normalized data

LungCellAtlas / HLCA_reproducibility

This repository contains all code used for the Human Lung Cell Atlas project.

MIT License

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Request for non-SCANVI normalized data #15

Closed annaKett closed 7 months ago

annaKett commented 10 months ago

Hello all, I would like to use the metacells algorithm https://github.com/tanaylab/metacells to aggregate the cells to 'pseudo cells'. To run metacells, I need raw (integer) counts that are not corrected for sampling depth. In adata.raw.X, I find those integer counts, however, I am not sure whether these are SCANVI corrected or not - they are not, right? Thank you so much for your support, enjoy the holidays!

LisaSikkema commented 9 months ago

Hey @annaKett, so sorry for the late reply (currently on maternity leave). The counts are indeed not corrected!