CellTree: an R/bioconductor package to infer the hierarchical structure of cell populations from single-cell RNA-seq data
| Autor: | David duVerle, Hiroyuki Aburatani, Sohiya Yotsukura, Seitaro Nomura, Koji Tsuda |
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| Jazyk: | angličtina |
| Rok vydání: | 2016 |
| Předmět: |
0301 basic medicine
Human stem cell RNA-Seq Computational biology Biology Biochemistry Bioconductor 03 medical and health sciences Structural Biology Cell differentiation Cell heterogeneity Humans Molecular Biology Single-cell RNA-seq Structure (mathematical logic) Sequence Analysis RNA Applied Mathematics Dimensionality reduction Stem Cells Document analysis Data science Expression (mathematics) Computer Science Applications 030104 developmental biology Tree structure RNA DNA microarray Software |
| Zdroj: | BMC Bioinformatics |
| ISSN: | 1471-2105 |
| Popis: | 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. |
| Databáze: | OpenAIRE |
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