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scFAIR manuscript

Material and source code for the scFAIR manuscript

📰Manuscript: TBD

📜Preprint: TBD

📅Data: See data/

📊Web portal: sc-fair.org (Sources: git repo)

Citation

TBD

I. Manuscript Figures

All manuscript figures are reproducible through scripts deposited here

II. Preprocessing scripts

1. Single-cell brain atlases

All annotated and curated atlases were downloaded as .h5ad files and deposited in the data/ folder.
It comprises:

all_neurons_BgeeUpdated.h5ad Human Allen brain atlas (only neurons, 2'480'956 cells, Bgee curated) downloaded from [https://www.bgee.org/ftp/external_data/human_brain_cell_atlas/](here)
all_non_neurons_BgeeUpdated.h5ad Human Allen brain atlas (only non-neurons, 888'263 cells, Bgee curated) downloaded from [https://www.bgee.org/ftp/external_data/human_brain_cell_atlas/](here)
Mus_musculus_SRP467631_droplet_based.h5ad Mouse brain atlas (Ensembl 113 (GRCm39), 4'041'295 cells, Bgee curated) downloaded from [https://www.bgee.org/ftp/bgee_v16_0/collaboration/scFAIR/h5ad/](here)

2. Running SAMap

See samap/ dedicated page.