A Bayesian mixture model for clustering droplet-based single-cell transcriptomic data from population studies. View Full Text


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2019-12

AUTHORS

Zhe Sun, Li Chen, Hongyi Xin, Yale Jiang, Qianhui Huang, Anthony R Cillo, Tracy Tabib, Jay K Kolls, Tullia C Bruno, Robert Lafyatis, Dario A A Vignali, Kong Chen, Ying Ding, Ming Hu, Wei Chen

ABSTRACT

The recently developed droplet-based single-cell transcriptome sequencing (scRNA-seq) technology makes it feasible to perform a population-scale scRNA-seq study, in which the transcriptome is measured for tens of thousands of single cells from multiple individuals. Despite the advances of many clustering methods, there are few tailored methods for population-scale scRNA-seq studies. Here, we develop a Bayesian mixture model for single-cell sequencing (BAMM-SC) method to cluster scRNA-seq data from multiple individuals simultaneously. BAMM-SC takes raw count data as input and accounts for data heterogeneity and batch effect among multiple individuals in a unified Bayesian hierarchical model framework. Results from extensive simulation studies and applications of BAMM-SC to in-house experimental scRNA-seq datasets using blood, lung and skin cells from humans or mice demonstrate that BAMM-SC outperformed existing clustering methods with considerable improved clustering accuracy, particularly in the presence of heterogeneity among individuals. More... »

PAGES

1649

Identifiers

URI

http://scigraph.springernature.com/pub.10.1038/s41467-019-09639-3

DOI

http://dx.doi.org/10.1038/s41467-019-09639-3

DIMENSIONS

https://app.dimensions.ai/details/publication/pub.1113327762

PUBMED

https://www.ncbi.nlm.nih.gov/pubmed/30967541


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Download the RDF metadata as:  json-ld nt turtle xml License info

HOW TO GET THIS DATA PROGRAMMATICALLY:

JSON-LD is a popular format for linked data which is fully compatible with JSON.

curl -H 'Accept: application/ld+json' 'https://scigraph.springernature.com/pub.10.1038/s41467-019-09639-3'

N-Triples is a line-based linked data format ideal for batch operations.

curl -H 'Accept: application/n-triples' 'https://scigraph.springernature.com/pub.10.1038/s41467-019-09639-3'

Turtle is a human-readable linked data format.

curl -H 'Accept: text/turtle' 'https://scigraph.springernature.com/pub.10.1038/s41467-019-09639-3'

RDF/XML is a standard XML format for linked data.

curl -H 'Accept: application/rdf+xml' 'https://scigraph.springernature.com/pub.10.1038/s41467-019-09639-3'


 

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