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

ABSTRACT:

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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. Graph

SUBMITTER: Julia M 

PROVIDER: S-EPMC4595899 | biostudies-literature | 2015 Oct

REPOSITORIES: biostudies-literature