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Prepare annotated Visium HD data #9

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csangara opened this issue Jun 11, 2024 · 0 comments · May be fixed by #13
Open
3 of 5 tasks

Prepare annotated Visium HD data #9

csangara opened this issue Jun 11, 2024 · 0 comments · May be fixed by #13

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@csangara
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csangara commented Jun 11, 2024 •
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  • Download whole brain mouse transcriptomics data and metadata from Allen Brain Institute
  • Subsample single-cell dataset to ~150,000 cells
  • Download mouse Visium HD data from 10x Genomics
  • Run cell2location to deconvolve Visium HD data using the reference atlas
  • Upload Visium HD data in correct format
@csangara csangara linked a pull request Jun 12, 2024 that will close this issue
Annotate Visium HD with cell2location #13
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Annotate Visium HD with cell2location saeyslab/spatial_ccc_experiments
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@csangara