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  "Package": "scOntoMatch",
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  "Title": "Aligning Ontology Annotation Across Single Cell Datasets with\n'scOntoMatch'",
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  "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\ndifficult to compare scRNA-seq datasets at scale. Leveraging\nthe ontology system for defining cell type hierarchy,\n'scOntoMatch' aims to align cell type annotations to make them\ncomparable across studies. The alignment involves two core\nsteps: first is to trim the cell type tree within each dataset\nso each cell type does not have descendants, and then map cell\ntype labels cross-studies by direct matching and mapping\ndescendants to ancestors. Various functions for plotting cell\ntype trees and manipulating ontology terms are also provided.\nIn the Single Cell Expression Atlas hosted at EBI, a compendium\nof datasets with curated ontology labels are great inputs to\nthis package.",
  "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",
  "VignetteBuilder": "knitr",
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  "Repository": "https://papatheodorou-group.r-universe.dev",
  "Date/Publication": "2023-10-27 12:36:33 UTC",
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  "Author": "Yuyao Song [aut, cre, ctb],\nIrene Papatheodorou [aut, ths]",
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    "email": "ysong@ebi.ac.uk",
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    "description": "PhD student at EMBL-EBI, Computational genomics / Bioinformatics / Single Cell Transcriptomics",
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    "description": "Decoding phenotypes using single cell genomics "
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    "getOntologyId",
    "getOntologyName",
    "getOntoMapping",
    "getOntoMinimal",
    "getOntoMultiMapping",
    "getSeuratRds",
    "ontoMinimal",
    "ontoMultiMatch",
    "ontoMultiMinimal",
    "ontoTranslate",
    "plotMatchedOntoTree",
    "plotOntoTree"
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  "_help": [
    {
      "page": "check_ontology_translate",
      "title": "make sure ontology names are all translated to ontology ids while warning, consider manual reannotation",
      "topics": [
        "check_ontology_translate"
      ]
    },
    {
      "page": "fill_query",
      "title": "Get a names list of ontology and id by id",
      "topics": [
        "fill_query"
      ]
    },
    {
      "page": "getOntologyId",
      "title": "Get a names list of ontology and id by name",
      "topics": [
        "getOntologyId"
      ]
    },
    {
      "page": "getOntologyName",
      "title": "Get a names list of ontology and id by id",
      "topics": [
        "getOntologyName"
      ]
    },
    {
      "page": "getOntoMapping",
      "title": "match ontology terms by direct mapping and mapping descendants to ancestors",
      "topics": [
        "getOntoMapping"
      ]
    },
    {
      "page": "getOntoMinimal",
      "title": "match descendant terms to ancestor terms within a dataset",
      "topics": [
        "getOntoMinimal"
      ]
    },
    {
      "page": "getOntoMultiMapping",
      "title": "Match descendants to ancestors in multiple ontology id lists",
      "topics": [
        "getOntoMultiMapping"
      ]
    },
    {
      "page": "getSeuratRds",
      "title": "read in seurat object .rds files as a named list of seurat object",
      "topics": [
        "getSeuratRds"
      ]
    },
    {
      "page": "ontoMinimal",
      "title": "get the minimal ontology tree of a dataset by reducing descendant terms to ancestor terms return obj meta.data[[\"cell_ontology_base\"]] storing the reduced ontology annotation",
      "topics": [
        "ontoMinimal"
      ]
    },
    {
      "page": "ontoMultiMatch",
      "title": "Core function of scOntoMatch Match the ontology annotation of multiple seurat objects",
      "topics": [
        "ontoMultiMatch"
      ]
    },
    {
      "page": "ontoMultiMinimal",
      "title": "get the minimal ontology tree of a list of seurat objects by reducing descendant terms to ancestor terms return a named list of seurat objects with meta.data[[\"cell_ontology_base\"]] storing the reduced ontology annotation",
      "topics": [
        "ontoMultiMinimal"
      ]
    },
    {
      "page": "ontoTranslate",
      "title": "translate named list of obj_list to named list of cell ontology ids per obj",
      "topics": [
        "ontoTranslate"
      ]
    },
    {
      "page": "plotMatchedOntoTree",
      "title": "Plot a ontology tree with matched ontology from ontoMatch",
      "topics": [
        "plotMatchedOntoTree"
      ]
    },
    {
      "page": "plotOntoTree",
      "title": "Plot a tree representation of ontology terms",
      "topics": [
        "plotOntoTree"
      ]
    }
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  "_readme": "https://github.com/papatheodorou-group/scontomatch/raw/HEAD/README.md",
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      "title": "scOntoMatch_vignette",
      "author": "Yuyao Song",
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        "Load data",
        "Match ontology annotation",
        "Trim the ontology tree per dataset",
        "Ontology tree for individual dataset",
        "Match ontology annotation cross datasets",
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