CRAN/E | scOntoMatch

scOntoMatch

Aligning Ontology Annotation Across Single Cell Datasets with 'scOntoMatch'

Installation

About

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.

github.com/Papatheodorou-Group/scOntoMatch
Bug report File report

Key Metrics

Version 0.1.1
R ≥ 3.5
Published 2023-10-27 343 days ago
Needs compilation? no
License MIT
License File
CRAN checks scOntoMatch results

Downloads

Yesterday 5 -38%
Last 7 days 37 -30%
Last 30 days 189 -11%
Last 90 days 551 +3%
Last 365 days 2.497 +56%

Maintainer

Maintainer

Yuyao Song

Authors

Yuyao Song

aut / cre / ctb

Irene Papatheodorou

aut / ths

Material

README
Reference manual
Package source

Vignettes

scOntoMatch_vignette

macOS

r-release

arm64

r-oldrel

arm64

r-release

x86_64

r-oldrel

x86_64

Windows

r-devel

x86_64

r-release

x86_64

r-oldrel

x86_64

Old Sources

scOntoMatch archive

Depends

R ≥ 3.5

Imports

ontologyIndex
ontologyPlot
purrr

Suggests

knitr
devtools
SeuratObject