Sincell: an R/Bioconductor package for statistical assessment of cell-state hierarchies from single-cell RNA-seq

Bioinformatics. 2015 Oct 15;31(20):3380-2. doi: 10.1093/bioinformatics/btv368. Epub 2015 Jun 22.


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 can 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 A detailed manual and a vignette are provided with the package.


Supplementary information: Supplementary data are available at Bioinformatics online.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms
  • Cell Differentiation / genetics*
  • Data Interpretation, Statistical
  • Gene Expression Profiling*
  • Sequence Analysis, RNA*
  • Single-Cell Analysis
  • Software*