Article

Nextflow Pipeline for Visium and H&E Data from Patient-Derived Xenograft Samples

2023-07-30

Abstract excerpt

<h4>Highlights</h4> We have developed an automated data processing pipeline to quantify mouse and human data from patient-derived xenograft samples assayed by Visium spatial transcriptomics with matched hematoxylin and eosin (H&E) stained image. We enable deconvolution of reads with Xenome, quantification of spatial gene expression from host and graft species with Space Ranger, extraction of B-allele frequencies,...

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Literature Corpus work: c536ad43-436b-5e03-ac3a-eaaa0d904769
DOI: 10.1101/2023.07.27.550727

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