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Annotating cell types in human single-cell RNA-seq data with CellO.

ABSTRACT: Cell type annotation is important in the analysis of single-cell RNA-seq data. CellO is a machine-learning-based tool for annotating cells using the Cell Ontology, a rich hierarchy of known cell types. We provide a protocol for using the CellO Python package to annotate human cells. We demonstrate how to use CellO in conjunction with Scanpy, a Python library for performing single-cell analysis, annotate a lung tissue data set, interpret its hierarchically structured cell type annotations, and create publication-ready figures. For complete details on the use and execution of this protocol, please refer to Bernstein et al. (2021).

SUBMITTER: Bernstein MN

PROVIDER: S-EPMC8379521 | biostudies-literature | 2021 Sep

REPOSITORIES: biostudies-literature

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Annotating cell types in human single-cell RNA-seq data with CellO.

Bernstein Matthew N MN Dewey Colin N CN

STAR protocols 20210817 3

Cell type annotation is important in the analysis of single-cell RNA-seq data. CellO is a machine-learning-based tool for annotating cells using the Cell Ontology, a rich hierarchy of known cell types. We provide a protocol for using the CellO Python package to annotate human cells. We demonstrate how to use CellO in conjunction with Scanpy, a Python library for performing single-cell analysis, annotate a lung tissue data set, interpret its hierarchically structured cell type annotations, and cr ...[more]

PMID: 34458864

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