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
Config/pak/sysreqs: zlib1g-dev
Repository: https://papatheodorou-group.r-universe.dev
Date/Publication: 2023-10-27 12:36:33 UTC
RemoteUrl: https://github.com/papatheodorou-group/scontomatch
RemoteRef: HEAD
RemoteSha: 93799368f8fd3a569130368f239cc4c053ddbaeb
NeedsCompilation: no
Packaged: 2026-06-09 07:09:47 UTC; root
Author: Yuyao Song [aut, cre, ctb],
  Irene Papatheodorou [aut, ths]