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Sincell: Bioconductor package for the statistical assessment of cell-state hierarchies from single-cell RNA-seq data

By Miguel JuliĆ”, Amalio Telenti, Antonio Rausell

Posted 27 Jan 2015
bioRxiv DOI: 10.1101/014472 (published DOI: 10.1093/bioinformatics/btv368)

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 (combined or not with a dimensionality reduction step), and ii) a graph-building algorithm (optionally making use of a cells-clustering step). Sincell R package implements a methodological toolbox allowing flexible workflows under such framework. Furthermore, Sincell contributes new algo-rithms 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. Sincell functionalities are illustrated in a real case study where its ability to discriminate noisy from stable cell-state hierarchies is demonstrated. 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 vignette describing functions and workflows is provided with the package.

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