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Merge pull request #307 from AlexsLemonade/allyhawkins/update-no-cell…
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Update FAQ for samples with missing cell type reports
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allyhawkins authored May 7, 2024
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Expand Up @@ -135,13 +135,8 @@ Most single-cell and single-nuclei RNA-seq libraries available on the portal wil
For more information on where to find the cell type annotations, refer to section(s) describing {ref}`SingleCellExperiment file contents <sce_file_contents:singlecellexperiment sample metadata>` and/or {ref}`AnnData file contents <sce_file_contents:anndata cell metrics>`.
If cell type annotation was performed, a supplemental cell type report (`SCPCL000000_celltype-report.html`) will be included in the download.

There are a few scenarios where cell type annotation was not performed, which means processed objects will not include cell type annotations, and the download will not include a cell type report.

- Cell type annotation is not performed for cell line samples.
- Cell type annotation is not performed on libraries with an insufficient number of cells.
The processed objects on which cell type annotation is performed must contain at least 30 cells to assign cell types with `CellAssign` and at least 2 cells to assign cell types with `SingleR`.
This means that in some rare cases there will not be enough cells remaining in the processed object for cell type annotation to be performed.

Cell type annotation is not performed on samples derived from cell lines.
This means processed objects will not include cell type annotations, and the download will not include a cell type report.

## What if I want to use Seurat instead of Bioconductor?

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