Unknown

Dataset Information

0

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 |

REPOSITORIES: biostudies-literature

Json Xml

Similar Datasets

Unknown A Hybrid Clustering Algorithm for Identifying Cell Types from Single-Cell RNA-Seq Data.
| S-EPMC6409843 | biostudies-other
Unknown Discovering cell types using manifold learning and enhanced visualization of single-cell RNA-Seq data.
| S-EPMC8742092 | biostudies-literature
Unknown scAIDE: clustering of large-scale single-cell RNA-seq data reveals putative and rare cell types.
| S-EPMC7671411 | biostudies-literature
Unknown V-SVA: an R Shiny application for detecting and annotating hidden sources of variation in single-cell RNA-seq data.
| S-EPMC7267827 | biostudies-literature
Unknown SCRABBLE: single-cell RNA-seq imputation constrained by bulk RNA-seq data.
| S-EPMC6501316 | biostudies-literature
Unknown Single-cell RNA-seq reveals new types of human blood dendritic cells, monocytes, and progenitors.
| S-EPMC5775029 | biostudies-literature
Unknown Single cell RNA-seq of primary human glioblastomas
| S-ECPF-GEOD-57872 | biostudies-other
Unknown scID Uses Discriminant Analysis to Identify Transcriptionally Equivalent Cell Types across Single-Cell RNA-Seq Data with Batch Effect.
| S-EPMC7063229 | biostudies-literature
Unknown An Efficient and Flexible Method for Deconvoluting Bulk RNA-Seq Data with Single-Cell RNA-Seq Data.
| S-EPMC6830085 | biostudies-literature
Unknown scphaser: haplotype inference using single-cell RNA-seq data.
| S-EPMC5039928 | biostudies-literature