Dataset Information
Automated cell type discovery and classification through knowledge transfer.
Ontology highlight
ABSTRACT: Motivation
Recent advances in mass cytometry allow simultaneous measurements of up to 50 markers at single-cell resolution. However, the high dimensionality of mass cytometry data introduces computational challenges for automated data analysis and hinders translation of new biological understanding into clinical applications. Previous studies have applied machine learning to facilitate processing of mass cytometry data. However, manual inspection is still inevitable and becoming the barrier to reliable large-scale analysis.Results
We present a new algorithm called utomated ell-type iscovery and lassification (ACDC) that fully automates the classification of canonical cell populations and highlights novel cell types in mass cytometry data. Evaluations on real-world data show ACDC provides accurate and reliable estimations compared to manual gating results. Additionally, ACDC automatically classifies previously ambiguous cell types to facilitate discovery. Our findings suggest that ACDC substantially improves both reliability and interpretability of results obtained from high-dimensional mass cytometry profiling data.Availability and implementation
A Python package (Python 3) and analysis scripts for reproducing the results are availability on https://bitbucket.org/dudleylab/acdc .Contact
brian.kidd@mssm.edu or joel.dudley@mssm.edu.Supplementary information
Supplementary data are available at Bioinformatics online.
SUBMITTER: Lee HC
PROVIDER: S-EPMC5447237 | biostudies-literature | 2017 Jun
REPOSITORIES: biostudies-literature
Publications
Automated cell type discovery and classification through knowledge transfer.
Bioinformatics (Oxford, England) 20170601 11
<h4>Motivation</h4>Recent advances in mass cytometry allow simultaneous measurements of up to 50 markers at single-cell resolution. However, the high dimensionality of mass cytometry data introduces computational challenges for automated data analysis and hinders translation of new biological understanding into clinical applications. Previous studies have applied machine learning to facilitate processing of mass cytometry data. However, manual inspection is still inevitable and becoming the barr ...[more]
