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Protocols for single-cell RNA-seq and spatial gene expression integration and interactive visualization.

ABSTRACT: There is a wealth of software that utilizes single-cell RNA-seq (scRNA-seq) data to deconvolve spatial transcriptomic spots, which currently are not yet at single-cell resolution. Here we provide protocols for implementing Seurat and Giotto packages to elucidate cell-type distribution in our example human ureter scRNA-seq dataset. We also describe how to create a stand-alone interactive web application using Seurat libraries to visualize and share our results. For complete details on the use and execution of this protocol, please refer to Fink et al. (2022).¹.

SUBMITTER: Sona S

PROVIDER: S-EPMC9871342 | biostudies-literature | 2023 Mar

REPOSITORIES: biostudies-literature

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Protocols for single-cell RNA-seq and spatial gene expression integration and interactive visualization.

Sona Surbhi S Bradley Matthew M Ting Angela H AH

STAR protocols 20230119 1

There is a wealth of software that utilizes single-cell RNA-seq (scRNA-seq) data to deconvolve spatial transcriptomic spots, which currently are not yet at single-cell resolution. Here we provide protocols for implementing Seurat and Giotto packages to elucidate cell-type distribution in our example human ureter scRNA-seq dataset. We also describe how to create a stand-alone interactive web application using Seurat libraries to visualize and share our results. For complete details on the use and ...[more]

PMID: 36853708

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