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CellTree: an R/bioconductor package to infer the hierarchical structure of cell populations from single-cell RNA-seq data

BACKGROUND: Single-cell RNA sequencing is fast becoming one the standard method for gene expression measurement, providing unique insights into cellular processes. A number of methods, based on general dimensionality reduction techniques, have been suggested to help infer and visualise the underlyin...

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Detalles Bibliográficos
Autores principales: duVerle, David A., Yotsukura, Sohiya, Nomura, Seitaro, Aburatani, Hiroyuki, Tsuda, Koji
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2016
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5020541/
https://www.ncbi.nlm.nih.gov/pubmed/27620863
http://dx.doi.org/10.1186/s12859-016-1175-6
Descripción
Sumario:BACKGROUND: Single-cell RNA sequencing is fast becoming one the standard method for gene expression measurement, providing unique insights into cellular processes. A number of methods, based on general dimensionality reduction techniques, have been suggested to help infer and visualise the underlying structure of cell populations from single-cell expression levels, yet their models generally lack proper biological grounding and struggle at identifying complex differentiation paths. RESULTS: Here we introduce cellTree: an R/Bioconductor package that uses a novel statistical approach, based on document analysis techniques, to produce tree structures outlining the hierarchical relationship between single-cell samples, while identifying latent groups of genes that can provide biological insights. CONCLUSIONS: With cellTree, we provide experimentalists with an easy-to-use tool, based on statistically and biologically-sound algorithms, to efficiently explore and visualise single-cell RNA data. The cellTree package is publicly available in the online Bionconductor repository at: http://bioconductor.org/packages/cellTree/. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12859-016-1175-6) contains supplementary material, which is available to authorized users.