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scOntoMatch
View on CRAN: Click
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Download and install scOntoMatch package within the R console
Install from CRAN:
install.packages("scOntoMatch")
Install from Github:
library("remotes")
install_github("cran/scOntoMatch")
Install by package version:
library("remotes")
install_version("scOntoMatch", "0.1.1")
Attach the package and use:
library("scOntoMatch")
Maintained by
Yuyao Song
[Scholar Profile | Author Map]
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2022-06-27
Latest Update: 2022-06-27
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.
How to cite:
Yuyao Song (2022). scOntoMatch: Aligning Ontology Annotation Across Single Cell Datasets with 'scOntoMatch'. R package version 0.1.1, https://cran.r-project.org/web/packages/scOntoMatch
Previous versions and publish date:
0.1.0 (2022-06-27 17:00)
Other packages that cited scOntoMatch R package
View scOntoMatch citation profile
Other R packages that scOntoMatch depends,
imports, suggests or enhances
Functions, R codes and Examples using
the scOntoMatch R package
Some associated functions: check_ontology_translate . fill_query . getOntoMapping . getOntoMinimal . getOntoMultiMapping . getOntologyId . getOntologyName . getSeuratRds . ontoMinimal . ontoMultiMatch . ontoMultiMinimal . ontoTranslate . plotMatchedOntoTree . plotOntoTree .
Some associated R codes: functions.R . helper_functions.R . Full scOntoMatch package functions and examples
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