Package: scOntoMatch
Type: Package
Title: Aligning Ontology Annotation Across Single Cell Datasets with
        'scOntoMatch'
Version: 0.1.1
Authors@R: c(person(given = "Yuyao", family = "Song", email = "ysong@ebi.ac.uk", role = c("aut", "cre", "ctb")), person(given = "Irene", family = "Papatheodorou", email = "irenep@ebi.ac.uk", role = c("aut", "ths")))
Maintainer: Yuyao Song  <ysong@ebi.ac.uk>
Description: 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.
Imports: ontologyIndex, ontologyPlot, purrr
URL: https://github.com/Papatheodorou-Group/scOntoMatch
BugReports: https://github.com/Papatheodorou-Group/scOntoMatch/issues
License: MIT + file LICENSE
Encoding: UTF-8
RoxygenNote: 7.2.3
Depends: R(>= 3.5)
Suggests: knitr, devtools, SeuratObject
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2023-10-27 12:33:09 UTC; ysong
Author: Yuyao Song [aut, cre, ctb],
  Irene Papatheodorou [aut, ths]
Repository: CRAN
Date/Publication: 2023-10-27 12:50:02 UTC
Built: R 4.4.3; ; 2026-02-23 14:07:25 UTC; windows
