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. 2021 Oct;31(10):1913–1926. doi: 10.1101/gr.273300.120

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© 2021 Nieto et al.; Published by Cold Spring Harbor Laboratory Press

This article, published in Genome Research, is available under a Creative Commons License (Attribution-NonCommercial 4.0 International), as described at http://creativecommons.org/licenses/by-nc/4.0/.

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Figure 3. — Automated annotation of external human tumor-derived immune cells using the tumor immune atlas as reference. (A,B) UMAP representation of immune cell transcriptomes from a primary uveal melanoma colored by their predicted cell type/state based on the tumor immune reference (A) or using unsupervised clustering (B). (C) Marker correspondence (Jaccard index) between uveal melanoma clusters (B) and the cell type clusters of the reference atlas. (D,E) UMAP representation of immune cell transcriptomes from a primary ovarian carcinoma colored by predicted cell type/state (D, color code as in A) and after clustering (E). (F) Marker correspondence (Jaccard index) between the ovarian cancer clusters and the cell type clusters of the reference atlas. (G) UMAP representation of immune cells from two uveal melanoma liver metastasis colored by their predicted cell type (color code as in A). (H,I) UMAP representation of T cells isolated from a brain metastasis colored by their predicted cell type (H, color code as in A) and clonal expansion profiled through TCR genotyping (I).