Summary: Cell differentiation processes are achieved through a continuum of hierarchical intermediate cell-states that might be captured by single-cell RNA seq. Existing computational approaches for the assessment of cell-state hierarchies from single-cell data might be formalized under a general framework composed of i) a metric to assess cell-to-cell similarities (with or without a dimensionality reduction step), and ii) a graph-building algorithm (optionally making use of a cell clustering step). The Sincell R package implements a methodological toolbox allowing flexible workflows under such a framework. Furthermore, Sincell contributes new algorithms to provide cell-state hierarchies with statistical support while accounting for stochastic factors in single-cell RNA seq. Graphical representations and functional association tests are provided to interpret hierarchies. The functionalities of Sincell are illustrated in a real case study, which demonstrates its ability to discriminate noisy from stable cell-state hierarchies.

Availability and implementation:

Sincell is an open-source R/Bioconductor package available at http://bioconductor.org/packages/3.1/bioc/html/sincell.html. A detailed manual and vignette is provided with the package.

Contact: antonio.rausell@isb-sib.ch

Supplementary Information: Supplementary data are available at Bioinformatics online.