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 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/ .
Graduate School of Frontier Sciences at the University of Tokyo, 5-1-5 Kashiwa-no-ha, Kashiwa, Japan. dave@cb.k.u-tokyo.ac.jp.|Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science and Technology, 2-4-7 Aomi, Koto-ku, Tokyo, Japan. dave@cb.k.u-tokyo.ac.jp.
David A
DA
duVerle
Bioinformatics Center, Institute for Chemical Research, Kyoto University, Gokasho, Uji, Japan.
Sohiya
S
Yotsukura
Genome Science Division, Laboratory of Systems Biology and Medicine, Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Tokyo, Japan.
Seitaro
S
Nomura
Genome Science Division, Laboratory of Systems Biology and Medicine, Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Tokyo, Japan.
Hiroyuki
H
Aburatani
Graduate School of Frontier Sciences at the University of Tokyo, 5-1-5 Kashiwa-no-ha, Kashiwa, Japan. tsuda@k.u-tokyo.ac.jp.|Center for Materials Research by Information Integration, National Institute for Materials Science, 1-2-1 Sengen, Tsukuba, Japan. tsuda@k.u-tokyo.ac.jp.|Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science and Technology, 2-4-7 Aomi, Koto-ku, Tokyo, Japan. tsuda@k.u-tokyo.ac.jp.
Koji
K
Tsuda
D002454:Cell Differentiation; D006801:Humans; D012313:RNA / Q000235:genetics*; D017423:Sequence Analysis, RNA / Q000379:methods*; D013234:Stem Cells / Q000276:immunology*
D012313:RNA
Cell differentiation; Cell heterogeneity; Human stem cell; Single-cell RNA-seq