scOntoMatch: Aligning Ontology Annotation Across Single Cell Datasets with 'scOntoMatch'

Unequal granularity of cell type annotation makes it difficult to compare scRNA-seq datasets at scale. Leveraging the ontology system for defining cell type hierarchy, 'scOntoMatch' aims to align cell type annotations to make them comparable across studies. The alignment involves two core steps: first is to trim the cell type tree within each dataset so each cell type does not have descendants, and then map cell type labels cross-studies by direct matching and mapping descendants to ancestors. Various functions for plotting cell type trees and manipulating ontology terms are also provided. In the Single Cell Expression Atlas hosted at EBI, a compendium of datasets with curated ontology labels are great inputs to this package.

Version: 0.1.0
Depends: R (≥ 3.5)
Imports: ontologyIndex, ontologyPlot, purrr
Suggests: knitr, devtools, SeuratObject
Published: 2022-06-27
Author: Yuyao Song ORCID iD [aut, cre]
Maintainer: Yuyao Song <ysong at>
License: MIT + file LICENSE
NeedsCompilation: no
Materials: README
CRAN checks: scOntoMatch results


Reference manual: scOntoMatch.pdf
Vignettes: scOntoMatch_vignette


Package source: scOntoMatch_0.1.0.tar.gz
Windows binaries: r-devel:, r-release:, r-oldrel:
macOS binaries: r-release (arm64): scOntoMatch_0.1.0.tgz, r-oldrel (arm64): scOntoMatch_0.1.0.tgz, r-release (x86_64): scOntoMatch_0.1.0.tgz, r-oldrel (x86_64): scOntoMatch_0.1.0.tgz


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