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content/03.results.md

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@@ -179,7 +179,7 @@ In parallel to developing the ScPCA Portal, we launched the OpenScPCA project [@
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Thus far, we have added cell type annotations for two projects, `SCPCP000004` (neuroblastoma) and `SCPCP000015` (Ewing sarcoma), to the Portal based on OpenScPCA analyses.
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Figure {@fig:fig5}A displays, for example, a UMAP of all libraries in `SCPCP000004` highlighting this project's OpenScPCA annotations, which were derived using the `NBAtlas` dataset as a reference [@doi:10.1016/j.celrep.2024.114804].
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Unlike the consensus cell type annotations, the OpenScPCA annotations distinguish between normal and malignant cells and contain far fewer uncharacterized cells.
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Indeed, for `SCPCP000004`, the consensus cell type procedure labeled only ~43% of cells, but the OpenScPCA project labeled ~91% of cells, more than doubling the number of labeled cells.
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For example, for `SCPCP000004`, the consensus cell type procedure labeled ~80% of cells, but the OpenScPCA project labeled ~88% of cells.
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When OpenScPCA annotations are available, the Portal's summary cell type report also includes comparisons between the `scpca-nf` and OpenScPCA annotations.
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In an effort to identify potential malignant cells across all samples in the Portal, `scpca-nf` applies `InferCNV` [@url:https://github.com/broadinstitute/inferCNV] to estimate copy-number alterations (Figure {@fig:fig2}A) when enough normal cells are present in a library to serve as a reference (see Methods for details).

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