RT Journal Article SR Electronic T1 Sincell: Bioconductor package for the statistical assessment of cell-state hierarchies from single-cell RNA-seq data JF bioRxiv FD Cold Spring Harbor Laboratory SP 014472 DO 10.1101/014472 A1 Miguel JuliĆ” A1 Amalio Telenti A1 Antonio Rausell YR 2015 UL http://biorxiv.org/content/early/2015/01/27/014472.abstract AB 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 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. 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 manual and vignette describing functions and workflows is provided with the package.Contact: antonio.rausell{at}isb-sib.ch