Other packages > Find by keyword >

scOntoMatch  

Aligning Ontology Annotation Across Single Cell Datasets with 'scOntoMatch'
View on CRAN: Click here


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]
All associated links for this package
First Published: 2022-06-27
Latest Update: 2023-10-27
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. Accessed 05 Mar. 2026.
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
Complete documentation for scOntoMatch
Downloads during the last 30 days

Today's Hot Picks in Authors and Packages

roccv  
ROC for Cross Validation Results
Cross validate large genetic data while specifying clinical variables that should always be in the m ...
Download / Learn more Package Citations See dependency  
ClimClass  
Climate Classification According to Several Indices
Classification of climate according to Koeppen - Geiger, of aridity indices, of continentality indi ...
Download / Learn more Package Citations See dependency  
neat  
Efficient Network Enrichment Analysis Test
Includes functions and examples to compute NEAT, the Network Enrichment Analysis Test described in ...
Download / Learn more Package Citations See dependency  
pinp  
'pinp' is not 'PNAS'
A 'PNAS'-alike style for 'rmarkdown', derived from the 'Proceedings of the National Academy of Scie ...
Download / Learn more Package Citations See dependency  
imagefx  
Extract Features from Images
Synthesize images into characteristic features for time-series analysis or machine learning applicat ...
Download / Learn more Package Citations See dependency  
nextGenShinyApps  
Craft Exceptional 'R Shiny' Applications and Dashboards with Novel Responsive Tools
Nove responsive tools for designing and developing 'Shiny' dashboards and applications. The scripts ...
Download / Learn more Package Citations See dependency  

26,264

R Packages

223,360

Dependencies

70,244

Author Associations

26,265

Publication Badges

© Copyright since 2022. All right reserved, rpkg.net.  Based in Cambridge, Massachusetts, USA